From PDB file to simulate a solvated system

The program conn - creates the connectivity file - one of the corner stones of any MD program. This file  includes all the necessary information for energy calculations of a specific molecule. Other modules, (e.g. mini_pwl that minimizes the energy of the molecule) read a prepared connectivity file before starting the computations. We start with the description of the input to con and then continue to describe the internal structure of this important program. A sample input that creates a connectivity file for valine dipeptide is:

~
~ input for connectivity (valine dipeptide)
~
file poly name=(VALD.POLY) unit=10 read
file mono name=(ALL.MONO)  unit=11 read
file prop name=(ALL.PROP)  unit=12 read
file wcon name=(VALD.WCON) unit=13 wovr
action
*EOD
~


The above information can be typed interactively or stored in a file - conn.inp - and redirected to the conn  program :


conn < conn.inp > conn.out

The output of the program conn also can be redirected to some new text file (conn.out) or displayed directly on the terminal screen.

Here is the polymerization file VALD.POLY where you tell MOIL how many monomers you are joining and in what sequence (molecule):

~
MOLC=(VALD) #mon=3
NTR0 VAL CTR0
*EOD
~

The files ALL.PROP and ALL.MONO contain  data about atom properties (Van-der-Waals parameters, bonds, angles) and monomers description, respectively.

The  conn program extracts specific information from the above databases. Below is presented only a small part of  ALL.MONO  file which is related to the connectivity of this molecule (all other records will be not processed for this specific configuration). Every monomer's block starts with the description keyword MONO=(...). Keyword DONE marks the end description of the monomer's atoms. If monomer consist of more than one atom the section BOND ... DONE contains the information about  existing covalent bonds.


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~
~ Monomers file : ALL.MONO
~
...
~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~                    uncharged N-terminus
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~
~uncharged N-terminus (1)~~~~~~~~~~~~~~~~~~~~~~~~(OPLS)~~~
~
MONO=(NTR0) #prt=6  chrg=0.0
~
~                 X    O
~                 :    :
~    ME - C - N - CA...C...
~         |   |
~         O   H
~
UNIQ=(N)   PRTC=(NH)   NEXT
UNIQ=(H)   PRTC=(HN)   NEXT
UNIQ=(CA)  PRTC=(CAH)  NEXT
UNIQ=(ME)  PRTC=(CH3)
UNIQ=(C)   PRTC=(CO)
UNIQ=(O)   PRTC=(OC)
DONE
BOND
C-N* C-O C-ME
DONE
~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~    VAL              (OPLS)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MONO=(VAL)   #prt=9  chrg=-0.570
~
~                O
~                |
~       N - CA - C...N
~       |   |
~       H   CB - CG2
~           |
~           CG1
~
~why not CH3 instead of CH3G (maybe because of improper torsion)?
~
~
UNIQ=(N)    PRTC=(NH)
UNIQ=(H)    PRTC=(HN)
UNIQ=(CA)   PRTC=(CAH)
UNIQ=(CB)   PRTC=(CBH)
UNIQ=(CG1)  PRTC=(CH3G)
UNIQ=(CG2)  PRTC=(CH3)
UNIQ=(C)    PRTC=(CO)
UNIQ=(O)    PRTC=(OC)
UNIQ=(N)    PRTC=(NH)  NEXT
DONE
BOND
 N-H N-CA  CA-CB CB-CG1 CB-CG2
CA-C C-O C-N*
DONE
~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~                   uncharged C-terminus
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~
~uncharged C-terminus (1)~(not gly,pro,BU)~~~~~~~(OPLS)~~~
~
MONO=(CTR0) #prt=6 chrg=0.2
~
~           X    O   H
~       :   :    |   |
~    ...N...CA - C - N -ME
~
UNIQ=(C)   PRTC=(CO)    PREV
UNIQ=(O)   PRTC=(OC)    PREV
UNIQ=(CA)  PRTC=(CAH)   PREV
UNIQ=(N)   PRTC=(NH)
UNIQ=(H)   PRTC=(HN)
UNIQ=(ME)  PRTC=(CH3T)
DONE
BOND
N-H N-ME
DONE
~
~
...
*EOD

The file ALL.PROP  contains five major sections that describe specific properties of the molecules and start with specific keywords:

  1. PRTC : atom parameters (name, mass, charge, VdW parameters)
  2. BOND : covalent bonds
  3. ANGLE : dihedral angles
  4. TORSION : torsion angles
  5. IMPROPER : improper torsion angles

All of these sections are closed by the keyword DONE and at the end of database file the keyword *EOD should be present. The program conn will pick only the records which contain atoms from relevant monomers of  ALL.MONO . Other records will be ignored. Below we display only a part of the file ALL.PROP :


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~
~ Properties file : ALL.PROP
~
PRTC
PNAM=(NH)    PMAS=14.    PCHG=-0.570  PEPS=0.17    PSGM=3.250
PNAM=(HN)    PMAS=1.     PCHG=0.370   PEPS=0.0498  PSGM=0.30
PNAM=(CO)    PMAS=12.    PCHG=0.50    PEPS=0.105   PSGM=3.750
PNAM=(OC)    PMAS=16.    PCHG=-0.5    PEPS=0.21    PSGM=2.960
PNAM=(CAH)   PMAS=13.    PCHG=0.20    PEPS=0.080   PSGM=3.800
PNAM=(CH3T)  PMAS=15.    PCHG=0.200   PEPS=0.170   PSGM=3.800
PNAM=(CH3)   PMAS=15.    PCHG=0.00    PEPS=0.16    PSGM=3.9100
PNAM=(CH3G)  PMAS=15.    PCHG=0.00    PEPS=0.160   PSGM=3.910
PNAM=(CBH)   PMAS=13.    PCHG=0.00    PEPS=0.080   PSGM=3.850
...
DONE
~
BOND
CAH    CO     317.0    1.522
CBH    CO     317.0    1.522
CO     OC     570.0    1.229
CAH    CBH    260.0    1.526
CAH    NH     337.0    1.449
NH     HN     434.0    1.010
CO     CH3    317.0    1.522
CO     NH     490.0    1.335
CBH    CH3    260.0    1.526
CBH    CH3G   260.0    1.526
CH3T   NH     337.0    1.449
CAH    CH3    260.0    1.526
...
DONE
~
ANGLE
CH3    CO     OC     80.0     120.4
OC     CO     NH     80.0     122.9
CO     NH     HN     35.0     119.8
CO     NH     CAH    50.0     121.9
CAH    NH     HN     38.0     118.4
NH     CAH    CO     63.0     110.1
CAH    CO     OC     80.0     120.4
CO     NH     CH3T   50.0     121.9
CH3T   NH     HN     38.0     118.4
CAH    CO     NH     70.0     116.6
CH3    CO     NH     70.0     116.6
NH     CAH    CBH    80.0     109.7
CAH    CBH    CH3    63.0     111.5
CAH    CBH    CH3G   63.0     111.5
CH3    CBH    CH3G   63.0     111.5
CBH    CAH    CO     63.0     111.1
...
DONE
~
TORSION
CH3    CO     NH     HN     0.0      2.5      0.0       2  -1.0
OC     CO     NH     HN     0.0      2.5      0.0       2  -1.0
CH3    CO     NH     CAH    0.0      2.5      0.0       2  -1.0
OC     CO     NH     CAH    0.0      2.5      0.0       2  -1.0
OC     CO     NH     CH3T   0.0      2.5      0.0       2  -1.0
CAH    CO     NH     CH3T   0.0      2.5      0.0       2  -1.0
CAH    CO     NH     HN     0.0      2.5      0.0       2  -1.0
OC     CO     CAH    NH     0.0      0.0      0.1       3  -1.0
CO     NH     CAH    CBH    0.0      0.0      0.0       3   0.0
HN     NH     CAH    CBH    0.0      0.0      0.0       3   0.0
CO     NH     CAH    CO     0.0      0.0      0.0       3   0.0
HN     NH     CAH    CO     0.0      0.0      0.0       3   0.0
NH     CAH    CBH    CH3G   0.0      0.0      0.5       3   1.0
OC     CO     CAH    CBH    0.0      0.0      0.1       3  -1.0
NH     CO     CAH    CBH    0.0      0.0      0.0       2   0.0
...
DONE
~
IMPROPER
NH     CAH    CO     HN     45.0     0.0
NH     CH3T   CO     HN     45.0     0.0
CO     CAH    OC     NH     100.0    0.0
CO     CH3    OC     NH     100.0    0.0
CAH    NH     CO     CBH    55.0     35.26
CBH    CAH    CH3    CH3G   55.0     35.26
...
DONE
~
*EOD

Here is the connectivity file  (VALD.WCON) which is the product of program conn : 








~ CONNECTIVITY FILE FOR MOLECULES: 

~ totmon npt nb nangl ntors nimp totex
totspe             
lestyp NBULK 

      3    14   
13    18    13     6   
31    20     0     1 

VALD 

~ Pointers to last particle of BULK 

    14 

~ Monomer names 

 NTR0 VAL  CTR0 

~ Pointers to last particle of monomer 

     3    11    14 

~ Properties of particles list : 

~pt mono ptid lesid ptnm   ptms   ptchg   epsgm6 epsgm12
ptwei 

     1   1  13   0
ME     15.00     .00000  
.47821E+02  .28586E+04  .10000E+01 

     2   1   9   0
C      12.00     .50000  
.34176E+02  .18022E+04  .10000E+01 

     3   1  10   0
O      16.00    -.50000  
.23769E+02  .61644E+03  .10000E+01 

     4   2   7   0
N      14.00    -.57000  
.28308E+02  .97175E+03  .10000E+01 

     5   2   8   0
H       1.00     .37000  
.00000E+00  .00000E+00  .10000E+01 

     6   2  11   0
CA     13.00     .20000  
.31040E+02  .17032E+04  .10000E+01 

     7   2  49   0
CB     13.00     .00000  
.32282E+02  .18422E+04  .10000E+01 

     8   2  26   0 CG1   
15.00     .00000   .47821E+02  .28586E+04 
.10000E+01 

     9   2  13   0 CG2   
15.00     .00000   .47821E+02  .28586E+04 
.10000E+01 

    10   2   9   0
C      12.00     .50000  
.34176E+02  .18022E+04  .10000E+01 

    11   2  10   0
O      16.00    -.50000  
.23769E+02  .61644E+03  .10000E+01 

    12   3   7   0
N      14.00    -.57000  
.28308E+02  .97175E+03  .10000E+01 

    13   3   8   0
H       1.00     .37000  
.00000E+00  .00000E+00  .10000E+01 

    14   3  12   0 ME    
15.00     .20000   .45249E+02  .24829E+04 
.10000E+01 

~ Bonds list: 

~ ib1 ib2 kbond req 

     1     2  
317.0000     1.5220 

     2     3  
317.0000     1.2290 

     2     4  
317.0000     1.3350 

     4     6  
260.0000     1.4490 

     4     5  
337.0000     1.0100 

     6     7  
260.0000     1.5260 

     6    10  
317.0000     1.5220 

     7     9  
260.0000     1.5260 

     7     8  
260.0000     1.5260 

    10    12  
490.0000     1.3350 

    10    11  
570.0000     1.2290 

    12    14  
337.0000     1.4490 

    12    13  
434.0000     1.0100 

~ Angles list: 

~ iangl1 iangl2 iangl3 kangl angleq 

     1     2    
3   80.00000  120.40000 

     1     2    
4   50.00000  121.90000 

     3     2    
4   80.00000  122.90000 

     2     4    
5   35.00000  119.80000 

     2     4    
6   50.00000  121.90000 

     5     4    
6   38.00000  118.40000 

     4     6    
7   80.00000  109.70000 

     4     6    10  

63.00000  110.10000 

     7     6    10  
63.00000  111.10000 

     6     7    
8   63.00000  111.50000 

     6     7    
9   63.00000  111.50000 

     8     7    
9   63.00000  111.50000 

     6    10    11  
80.00000  120.40000 

     6    10    12  
70.00000  116.60000 

    11    10    12  
80.00000  122.90000 

    10    12    13  
35.00000  119.80000 

    10    12    14  
50.00000  121.90000 

    13    12    14  
38.00000  118.40000 

~ Torsions list: 

~ itor1 itor2 itor3 itor4 period ktors1
ktors2                 
ktors3 phase 

     1     2    
4     5     2     
.0000     2.5000      .0000 -1.000 

     1     2    
4     6     2     
.0000     2.5000      .0000 -1.000 

     3     2    
4     5     2     
.0000     2.5000      .0000 -1.000 

     3     2    
4     6     2     
.0000     2.5000      .0000 -1.000 

     4     6    
7     8     3     
.0000      .0000      .5000 -1.000 

     4     6    
7     9     3     
.0000      .0000      .5000  1.000


     4     6   
10    11     3     
.0000      .0000      .1000 -1.000 

     8     7    
6    10     3     
.0000      .0000      .5000  1.000


     9     7    
6    10     3     
.0000      .0000      .5000  1.000


     6    10    12   
13     2      .0000    
2.5000      .0000 -1.000 

     6    10    12   
14     2      .0000    
2.5000      .0000 -1.000 

    11    10    12   
13     2      .0000    
2.5000      .0000 -1.000 

    11    10    12   
14     2      .0000    
2.5000      .0000 -1.000 

~ Improper torsion properties: 

~iimp1 iimp2 iimp3 iimp4 kimp impeq 

     2     1    
3     4   .10000000E+03   .00000000E+00 

     4     6    
2     5   .45000000E+02   .00000000E+00 

     6     4   
10     7   .55000000E+02   .35260000E+02 

     7     6    
9     8   .55000000E+02   .35260000E+02 

    10     6    11   
12   .10000000E+03   .00000000E+00 

    12    14    10   
13   .45000000E+02   .00000000E+00 

~ Exclusion list 1-2 1-3, set as followed: 

~ atom number, number of exclusions and list 

     1     3 

     2    3    4 

     2     4 

     3    4    5    6


     3     1 

     4 

     4     4 

     6    5    7   10


     5     1 

     6 

     6     6 

     7   10    8   
9   11   12 

     7     3 

     9    8   10 

     8     1 

     9 

    10     4 

    12   11   13   14 

    11     1 

    12 

    12     2 

    14   13 

    13     1 

    14 

~ Special list 1-4  set as followed: 

~ atom number, number of exclusions and list 

     1     2 

     5    6 

     2     2 

     7   10 

     3     2 

     5    6 

     4     4 

     8    9   11   12 

     5     2 

     7   10 

     6     2 

    13   14 

     7     2 

    11   12 

     8     1 

    10 

     9     1 

    10 

    11     2 

    13   14 








To perform  (?)  energy evaluation the connectivity file must be supplemented
by an atomic coordinates' file. The CHARMM coordinates file format is used in  MOIL.
Below a single configuration for the valine dipeptide is provided ( Cartesian coordinates
in CHARMM format). 








* 

*  initial structure, valine dipeptide in helix conformation 

* 

   14 

    1    1 NTR0 ME   
-0.02717   3.41564   0.00488 VALD 1     15.03500


    2    1 NTR0 C     
0.04827   1.91708  -0.24090 VALD 1     12.01100 

    3    1 NTR0 O     
0.67142   1.46396  -1.20000 VALD 1     15.99940 

    4    2 VAL  N    
-0.58751   1.13019   0.63714 VALD 1     14.00670


    5    2 VAL  H    
-1.05774   1.57408   1.37031 VALD 1     
1.00800 

    6    2 VAL  CA    -0.63665 
-0.33703   0.58146 VALD 1     13.01900 

    7    2 VAL  CB    -1.49790 
-0.83846  -0.61850 VALD 1     15.03500 

    8    2 VAL  CG1   -2.91731 
-0.28641  -0.56404 VALD 1      0.00000 

    9    2 VAL  CG2   -1.57439 
-2.35741  -0.74809 VALD 1      0.00000 

   10    2 VAL  C     
0.70303  -1.08091   0.68144 VALD 1     12.01100 

   11    2 VAL  O     
0.92822  -1.80836   1.64793 VALD 1     15.99940 

   12    3 CTR0 N      1.61106 
-0.91246  -0.28244 VALD 1     14.00670 

   13    3 CTR0 H      1.39819 
-0.28295  -1.00480 VALD 1      1.00800 

   14    3 CTR0 ME     2.93848 
-1.59696  -0.26438 VALD 1     15.03500 









MOIL does not provide a module to generate automatically coordinate files. It allows
however to process data from other sources. One important source for the coordinate files
are Protein Data Bank. The coordinates are stored in a PDB format which requires
adjustments. Both CHARMM and PDB formats are records of fixed length and transformation of
the coordinates is not difficult, but some of the PDB atom or residue names should be
edited to be consistent with the MOIL databases ( files ALL.PROP
and ALL.MONO  ). 



The database information about proteins are stored in text files in which every record
(line) begins with a keyword. A full description of all records can be find in the
PDB  from The Research Collaboratory for Structural Bioinformatics (RCSB)  [http://www.rcsb.org/index.html]. Below we will
consider one complicated example - converting the PDB data file of myglobin into CHARMM
format. The myoglobin PDB data file - pdb1mbd.ent
- which is the deoxy-form. To extract the coordinate data file only the records which
begins with ATOM and HETATM keywords are important. All other records
are ignored. 



There are several steps in the preparation of the data for MOIL: 


    
  
  1. exclude all duplicate records (some atoms appear more than once in the cristalography
    maps);
    2. 
  
  2. editing of some of the PDB atoms and residues names;
    3. 
  
  3. adding  N-terminus and C-terminus to the protein molecule;
    4. 
  
  4. excluding or editing of all water molecules that belong with protein molecule;
    5. 
  
  5. creating a new text file with monomer information of the molecule (*.poly
    file);
    6. 
  
  6. adding of the missing hydrogen atoms (Program puth)
    to the PDB structure and writing of all information in the CHARMM format;
    7. 
  
  7. optional solvation of the protein molecule (Program solvatecrd)
    which will fill the protein outer space of the rectangular box with water molecules.
    8. 







Removing some of the multiple doubling records of the same atom from a PDB file can be
done manually or using a program ( for example  pdb2puth).
The records with labels 2,3 .. or B,C... in column 17 should be deleted manually and the
label 1 or A should be replaced by a space character. We create a new coordinate file 1mbd_edit.ent from source file - pdb1mbd.ent . The records with atom numbers 106,108,688,690,714,716,1204,1206,1208,
1210,1212,1214,1216 were deleted since they are repeats of previous records and
respective previous records were edited to have a space character in column 17. Terminal
residues are separate issues that need to be addressed before using MOIL. Before the
first atom we have added a record which describe the N-terminus of the protein molecule. 



The coordinates for the N-terminus has a special value (9999.99): 








ATOM      0  HX2 NTER   
0    9999.99 9999.99 9999.99   1.00 28.18 










which will tell to the next program (Program puth) to add the
correct one. Also the index of the monomer NTER was stored to 0 to be
different from the next one (VAL  1). In order to add the C-terminus for the
protein molecule in the record ATOM   1230 the monomer name was changed
from GLY to CTRG and the monomer index was changed to 0 (or can
be other number different from previous and next residues numbers): 










ATOM   1230  OX2 CTRG    0     
-3.627  24.845  -7.563  8.00 44.30      1MBD1309









The next PDB record (keyword TER) was deleted because previous edited 
record specifies type of C-terminus. 



Water molecules which are included in the PDB file can be removed or transformed to the
MOIL format. 

The transformation means that all the atoms of oxygen should be renamed into OH2
and water molecules into TIP3.  Also is necessary to remove all the
multiple-duplicate records of water ( in our case HETATM 1371, 1374). 



The above operations on  removing of the multiple records can be done in
interactive mode using the Swiss-PdbViewer (http://www.expasy.ch/spdbv/).
However the NTER and CTRG records should be added manually after this,
because this program remove completely such records from PDB format. 



Next step is editing some of the atoms and residues (monomers) names from initial
source. The name of monomer residue S04 should be changed into SUL (HETATM
1620-1624). In the monomer HEM the FE atom should be shifted with
one position to right (ATOM1625). The names "N A", "N B",
"N C" and "N D" ( ATOM 1630, 1641, 1649, 1657)
should be changed to NA, NB, NC and ND to avoid the spaces in the name
of atoms (MOIL doesn't accept the spaces in the names). Also the residue name HEM
was changed in the HEM1 (HETATM 1625-1667), which is the internal name for the
monomer in the ALL.MONO file for the de-oxy form. HEME
should be used for the bonded form to a ligand. 



Note:  As alternative to the manual editing we are providing one
program (pdb2puth) which should do most of the above operations
automatically given the input PDB file. To get the same result as described above it is
necessary to call: 










pdb2puth < 1mbd_pdb2puth.inp > 1mbd_pdb2puth.log 



 






After processing the output file 1mbd.ent
contains the same information as in the edited manually 1mbd_edit.ent. 



To obtain the connectivity file one need to create a new file with monomers information
- file 1mbd.poly - or check the file 1mbd.poly which is created by the program (pdb2puth)
. The number and names of the monomers should be exact the same like the number and names
of the residues in the edited  1mbd_edit.ent
or the transformed 1mbd.ent PDB files. The input
for the *.poly files are free so it is not important how many monomers are in a
line but they should come in the same order as in the PDB file. In the case of the manual
creation of the file 1mbd.poly the sequence
records of the PDB file (keyword SEQRES )  are useful. 



Usually the PDB file don't contains information about the coordinates of the hydrogen
atoms. Adding of these records to the protein and to the water molecules can be done using
another MOIL utility - the program  puth - which also
transform the format of the PDB file into CHARMM coordinate one. However to run this
utility the connectivity file is needed. The connectivity file
can be obtained using program conn : 










conn < 1mbd_conn.inp > 1mbd_conn.log 








The program conn gets all the information about the files
directly from input (or from a redirected text file  1mbd_conn.inp ) and write all the step of
processing on the standard system output (or to a redirected text file  1mbd_conn.log ) . The input file should
contains as minimum the monomers ALL.MONO  ,
properties ALL.PROP database files and a description of
the structure in term of monomers 1mbd.poly .
As a result is created the file 1mbd.wcon which
incorporate all the necessary information about protein molecule. 



puth is a program to read pdb format file and to detect and to
place missing hydrogens as defined by the connectivity file. The algorithm is based on
covalent structure only and not on hydrogen bonds between donors and acceptors. For
example, hydrogens for a water molecules are placed in random directions (though
satisfying the covalent requirements of individual molecules). This seems to be quite
satisfactory, and bad contacts are corrected by a short minimization. 



Note that the program will halt if an atom other than hydrogen is missing. 



Atom numbers are not important and are not used, sequential monomer numbers are not
important too, however different monomers must have different monomer numbers. Of course
the order of the monomers must be as is in the poly file, the order of the
particles within a monomer is not important. 








puth < 1mbd_puth.inp >
1mbd_puth.log 










The  file 1mbd_puth.inp should specifies only the  connectivity
file 1mbd.wcon and the PDB file 1mbd.ent. The database files  ALL.MONO  and ALL.PROP are
not necessary to include anymore since the  connectivity file 1mbd.wcon contains all the data about monomers and
atom properties. 



The program  puth creates the new CHARMM coordinate file 1mbd.crd which have the same number of monomers
(residues) but larger number of atoms (because a new hydrogen atoms records is added to
the protein and water molecules). 



Both the connectivity 1mbd.wcon and
coordinate  1mbd.crd  files are enough
to start any dynamics simulations however minimization is highly recommended once
the placement of hydrogens is complete. 



Another useful utility (Program solvatecrd) is provided 
for full  solvating the molecule of interest. This program gets the CHARMM coordinate
file format and add the necessary amount of water molecules to fill the required
rectangular box. 








solvatecrd < 1mbd_solv.inp
> 1mbd_solv.log 








The input file 1mbd_solv.inp contains
four records which should be ordered in the following: 


    
  
  1. name of the file with water coordinates (../../moil.crd/watbox.crd)
    2. 
  
  2. name of the coordinate file with structure to be solvated (1mbd.crd)
    3. 
  
  3. name of the connectivity file for the structure to be solvated (1mbd.wcon)
    4. 
  
  4. name of the coordinate file with solvated structure to be created (1mbd_solv.crd)
    5. 
  
  5. name of the new poly file for the solvated structure to be created  (1mbd_solv.poly)
    6. 





  
After loading the protein structure is centered at the origin of coordinate. The
    remaining three records in the file describe the exclusion region and the dimension of the
    water box in all directions (x, y and z). The maximum length of the box is 100 in
    angstroms. The exclusion region D means that no molecules of water will be placed
    in the (-D,+D) interval for the corresponding axis. This is useful for solvating
    of the planar geometry objects - like lipid membranes. To avoid any exclusion region set
    the first number equal to zero. In addition to the solvated coordinate file 1mbd_solv.crd a new corresponding poly
    file 1mbd_solv.poly
    is created because the number of monomers was increased due adding of new water
    molecules.





To start the dynamics simulations it is necessary to create a new connectivity
file that correspond to new structure which consist of protein molecule and environmental
water molecules. Below is given an example of a new input for the program conn
: 








conn < 1mbd_conn_solv.inp
> 1mbd_conn_solv.log 










The resulting connectivity file 1mbd_solv.wcon
with previously created CHARMM coordinate file 1mbd_solv.crd
can be used for the energy minimization or dynamics simulations.