Disulfide bonds

Disulfide bonds are usually specified in a pdb file in the header lines in the following form:

SSBOND   1 CYS      3    CYS     22                                     1FSC 138
SSBOND   2 CYS     17    CYS     39                                     1FSC 139
SSBOND   3 CYS     41    CYS     52                                     1FSC 140
SSBOND   4 CYS     53    CYS     59                                     1FSC 141

This protein has 4 disulfide bonds that will need to be indicated to CHARMM. convpdb.pl automatically reads these records from the pdb file and passes the information on to CHARMM for energy calculations.

The best way to have SSBONDs is to let MMTSB tools make them, and keep track of them. However, if the SSBOND records are missing from the pdb, they can be added with several of the MMTSB tools (see ssbond flag for convpdb.pl documentation). SSBONDs can be removed as well.

The mmtsb CHARMM tools also have the -par argument to specify parameters that will be sent to CHARMM. For SSBONDs the bond can be specified by a CHARMM patch. There are many patches that add, delete, or change features of a chemical structure in charmm. In this case we would add some disulfide bonds to the structure between particular residues.

Using the ssbond flag

To add an ssbond explicitly:

convpdb -ssbond res1:res2 < pdbfile

Using the DISU patch

See the documentation for CHARMM parameters in mmtsb and the tutorials. A disulfide bond is specified in the parameters with the disu patch, and is used as in the following examples:

Disulfide bond between residues 3 and 22 as in the SSBOND number one above:
```
-par patch=disu:3:22             
```
Several disulfide bonds between residues 3 and 22, 17 and 39, 41 and 52, and 53 and 59 as in the SSBOND specifications above:
```
-par patch=disu:3:22_DISU:17:39_DISU:41:52_disu:53:59             
```

Disulfide tutorial (download)

This example demonstrates the conditioning of a raw pdb file 1fsc.pdb to use with the CHARMM tools, and the specifying of the disulfide bonds as specified in the raw pdb file header.

First look in the pdb file ( 1fsc.pdb) and find the SSBOND lines that specify the disulfide linkages. Look below the REMARKs and before the ATOMs.
Using those, one can construct the patch parameters to use in minCHARMM, enerCHARMM, etc.

The following script ( tutorial_disu) demonstrates the commands. One can download the script, change to to be executable, and execute it
OR
enter each command individually from the shell prompt.

#! /bin/csh 

if ( ! -d tutorial_disulfide ) mkdir tutorial_disulfide
cd  tutorial_disulfide
cp ../data/1fsc.pdb .

# Demonstrate how to make disulfide bonds in mmtsb tools
#
set pdb=1fsc
set pdb_H=${pdb}_H

# condition the pdb file, add hydrogens, remove hetero atoms and 
# crystal water molecules.
# This protein has 61 residues numbered 1 to 61, the rest is other stuff.
#
#########################################################
#      First try no disulfides
#
     echo -n "converting pdb, adding H,  "
convpdb.pl -out charmm22 -nohetero -nossbond < $pdb.pdb \
       | complete.pl - \
       >! $pdb_H.pdb
     echo "done ($pdb_H.pdb)"
# Use the patch parameter with CHARMM to get an energy of the structure
#  with the disulfide bonds made.
#
         echo -n "Initial Energy              no ssbond:   "
 enerCHARMM.pl < $pdb_H.pdb
#
#########################################################
#      disulfides from patches
#
         echo -n "Initial Energy no ssbond from patches:   "
enerCHARMM.pl -par patch=disu:3:22_DISU:17:39_DISU:41:52_disu:53:59 \
              < $pdb_H.pdb
#
#########################################################
#      automatic disulfides
#
     echo  "converting pdb automatic ssbonds, adding H,  "
convpdb.pl -out charmm22 -nohetero < $pdb.pdb | complete.pl - >! $pdb_H.pdb
     echo -n "Initial Energy       automatic ssbond:   "
enerCHARMM.pl < $pdb_H.pdb
#
#############################################################
# Short minimization
#
           echo -n "Minimizing  "
minCHARMM.pl -par sdsteps=50,minsteps=50 \
        -log min.log -elog emin.log -cmd min.inp \
        < $pdb_H.pdb \
        >! ${pdb_H}_min.pdb
      echo "done (${pdb_H}_min.pdb)"
      echo -n "Minimized Energy: "
enerCHARMM.pl < ${pdb_H}_min.pdb 

cd ..