From: wang (c00jsw00_at_nchc.org.tw)
Date: Tue Aug 01 2006 - 03:19:06 CDT
Dhiraj Srivastava ??:
> Hi all
> i want to simulate my protein whose pdb file has although only
> one chain but in vmd it looks like 2 chain as coordinates of some
> amino acid residues are missing. should i consider it as one chain or
> two? what about the patches at the end of the chain?
>
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153
Plz , felloing the script !
# 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
package require psfgen
# (2) Embed the psfgen commands in this script
# (3) Read topology file
topology top_all27_prot_lipid.inp
# (4) Build protein segment
segment A {
pdb myfile_frag1.pdb
}
# (5) Patch protein segment
patch DISU A:22 A:93
# (6) Read protein coordinates from PDB file
pdbalias atom ILE CD1 CD ;# formerly "alias atom ..."
pdbalias atom GLY OXT OT1 ;
pdbalias residue HIS HSE ;
coordpdb myfile_frag1.pdb A
# (7) Build water segment
#pdbalias residue HOH TIP3 ; # formerly "alias residue ..."
segment B {
pdb myfile_frag0.pdb
}
# (8) Read water coordinaes from PDB file
patch DISU B:22 B:128
patch DISU B:30 B:116
patch DISU B:77 B:95
patch DISU B:65 B:81
pdbalias atom ILE CD1 CD ;# formerly "alias atom ..."
pdbalias atom GLY OXT OT1 ;
pdbalias residue HIS HSE ;
coordpdb myfile_frag0.pdb B
# (9) Guess missing coordinates
guesscoord
# (10) Write structure and coordinate files
writepsf all.psf
writepdb all.pdb
# End of psfgen commands
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