BPTI Example

To actually run this demo requires

• the program psfgen from any NAMD distribution,
• the CHARMM topology and parameter files top_all22_prot.inp and par_all22_prot.inp from http://mackerell.umaryland.edu/charmm_ff.shtml, and
• the BPTI PDB file 6PTI.pdb available from the Protein Data Bank at http://www.pdb.org/ by searching for 6PTI and downloading the complete structure file in PDB format.

Building the BPTI structure

In this demo, we create the files bpti.psf and bpti.pdb in the output directory which can then be used for a simple NAMD simulation.

# File: bpti_example.tcl
# Requirements: topology file top_all22_prot.inp in directory toppar
#               PDB file 6PTI.pdb in current directory

# Create working directory; remove old output files
mkdir -p output
rm -f output/6PTI_protein.pdb output/6PTI_water.pdb

# (1) Split input PDB file into segments}
grep -v '^HETATM' 6PTI.pdb > output/6PTI_protein.pdb
grep 'HOH' 6PTI.pdb > output/6PTI_water.pdb

# (2) Embed the psfgen commands in this script
psfgen << ENDMOL

# (3) Read topology file
topology toppar/top_all22_prot.inp

# (4) Build protein segment
segment BPTI {
 pdb output/6PTI_protein.pdb
}

# (5) Patch protein segment
patch DISU BPTI:5 BPTI:55
patch DISU BPTI:14 BPTI:38
patch DISU BPTI:30 BPTI:51

# (6) Read protein coordinates from PDB file
pdbalias atom ILE CD1 CD    ; # formerly "alias atom ..."
coordpdb output/6PTI_protein.pdb BPTI

# (7) Build water segment
pdbalias residue HOH TIP3   ; # formerly "alias residue ..."
segment SOLV {
 auto none
 pdb output/6PTI_water.pdb
}

# (8) Read water coordinaes from PDB file
pdbalias atom HOH O OH2     ; # formerly "alias atom ..."
coordpdb output/6PTI_water.pdb SOLV

# (9) Guess missing coordinates
guesscoord

# (10) Write structure and coordinate files
writepsf output/bpti.psf
writepdb output/bpti.pdb

# End of psfgen commands
ENDMOL

Step-by-step explanation of the script:

(1) Split input PDB file into segments.

6PTI.pdb is the original file from the Protein Data Bank. It contains a single chain of protein and some PO4 and H2O HETATM records. Since each segment must have a separate input file, we remove all non-protein atom records using grep. If there were multiple chains we would have to split the file by hand. Create a second file containing only waters.

(2) Embed the psfgen commands in this script.

Run the psfgen program, taking everything until “ENDMOL” as input. You may run psfgen interactively as well. Since psfgen is built on a Tcl interpreter, you may use loops, variables, etc., but you must use $$ for variables when inside a shell script. If you want, run psfgen and enter the following commands manually.

(3) Read topology file.

Read in the topology definitions for the residues we will create. This must match the parameter file used for the simulation as well. Multiple topology files may be read in since psfgen and NAMD use atom type names rather than numbers in psf files.

(4) Build protein segment.

Actually build a segment, calling it BPTI and reading the sequence of residues from the stripped pdb file created above. In addition to the pdb command, we could specify residues explicitly. Both angles and dihedrals are generated automatically unless “auto none” is added (which is required to build residues of water). The commands “first” and “last” may be used to change the default patches for the ends of the chain. The structure is built when the closing } is encountered, and some errors regarding the first and last residue are normal.

(5) Patch protein segment.

Some patch residues (those not used to begin or end a chain) are applied after the segment is built. These contain all angle and dihedral terms explicitly since they were already generated. In this case we apply the patch for a disulfide link three separate times.

(6) Read protein coordinates from PDB file.

The same file used to generate the sequence is now read to extract coordinates. In the residue ILE, the atom CD is called CD1 in the pdb file, so we use “pdbalias atom” to define the correct name. If the segment names in the pdb file match the name we gave in the segment statement, then we don't need to specify it again; in this case we do specify the segment, so that all atoms in the pdb file must belong to the segment.

(7) Build water segment.

Build a segment for the crystal waters. The residue type for water depends on the model, so here we alias HOH to TIP3. Because CHARMM uses an additional H-H bond we must disable generation of angles and dihedrals for segments containing water. Then read the pdb file.

(8) Read water coordinates from PDB file.

Alias the atom type for water oxygen as well and read coordinates from the file to the segment SOLV. Hydrogen doesn't show up in crystal structures so it is missing from this pdb file.

(9) Guessing missing coordinates.

The tolopogy file contains default internal coordinates which can be used to guess the locations of many atoms, hydrogens in particular. In the output pdb file, the occupancy field of guessed atoms will be set to 0, atoms which are known are set to 1, and atoms which could not be guessed are set to -1. Some atoms are “poorly guessed” if needed bond lengths and angles were missing from the topology file. Similarly, waters with missing hydrogen coordinates are given a default orientation.

Write structure and coordinate files.

Now that all of the atoms and bonds have been created, we can write out the psf structure file for the system. We also create the matching coordinate pdb file. The psf and pdb files are a matched set with identical atom ordering as needed by NAMD.

Using generated files in NAMD.

The files bpti.pdb and bpti.psf can now be used with NAMD, but the initial coordinates require minimization first. The following is an example NAMD configuration file for the BPTI example.

# NAMD configuration file for BPTI

# molecular system
structure	output/bpti.psf

# force field
paratypecharmm	on
parameters	toppar/par_all22_prot.inp
exclude		scaled1-4
1-4scaling	1.0

# approximations
switching	on
switchdist	8
cutoff		12
pairlistdist	13.5
margin		0
stepspercycle	20

#integrator
timestep 1.0

#output
outputenergies	10
outputtiming	100
binaryoutput	no

# molecular system
coordinates	output/bpti.pdb

#output
outputname	output/bpti
dcdfreq		1000

#protocol
temperature	0
reassignFreq	1000
reassignTemp	25
reassignIncr	25
reassignHold	300

#script

minimize 1000

run 20000