From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Dec 06 2005 - 11:37:55 CST
I assume each ligand and the receptor complex has a unique segname?
Assuming this is true, I would do this:
package require psfgen
readpsf file.psf
coordpdb file.pdb
delatom ligand1-segname
writepsf file-new.psf
writepdb file-new.pdb
Let me know if this works for you.
On Dec 6, 2005, at 11:06 AM, Grace Shen wrote:
> Dear All:
>
> I have a.pdb and a.psf files which works fine. In a.pdb file, it
> contains two ligands and a receptor complex. Now I want to remove one
> ligand information from a.pdb file. How can I generate corresponding
> psf file? What I did is stated as followings:
>
> 1. Use VMD to modify the a.pdb file to remove the ligand and save as
> btemp.pdb file.
> 2. Use btemp.pgn script to generate b.pdb and b.psf file.
> --------b.pgn----------
> package require psfgen
> #topology lig12.rtf
> topology lig2.rtf
> topology /home1/lshen/Script/charmmInsightII/AMINOH.RTF
> topology /home1/lshen/Script/charmmInsightII/CHARMM_support.rtf
> segment U {pdb btemp.pdb}
> coordpdb btemp.pdb U
> guesscoord
> writepdb b.pdb
> writepsf b.psf
> eit
> ---------b.pgn--------
> 3. But I got the following error messages:
> --------------------
> Created by CHARMM version 22 0
> building segment U
> reading residues from pdb file eg5cw.pdb
> duplicate residue key 16
> ERROR: failed on residue GLY from pdb file
> duplicate residue key 19
> ERROR: failed on residue ILE from pdb file
> duplicate residue key 20
> ERROR: failed on residue GLN from pdb file
> duplicate residue key 25
> ERROR: failed on residue CYS from pdb file
> duplicate residue key 26
> ERROR: failed on residue ARG from pdb file
> ....
>
> Thanks,
>
> Grace
>
>
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