Re: Re: about psfgen

From: emilia.l.wu (
Date: Sat Jul 04 2009 - 10:53:18 CDT


Thank you for your reply, but the structure of the patched residues (res2 and res12) are fine,
it is the first residue ACE has the structure problem.
I can not attached my psf and pdb file here, I do not know why.



发件人: Ramya Gamini
发送时间: 2009-07-04 09:40:48
收件人: emilia.l.wu
抄送: namd-l
主题: Re: namd-l: about psfgen

On including new patches like you have in here- DISU, you must then include a line
regenerate angles dihedrals

for reference:

hope it helps

On Sat, Jul 4, 2009 at 8:59 AM, emilia.l.wu <> wrote:

Hi all,

I use? the psfgen script below to read a pdb file, guess some coordinates for missing atoms and get another pdb and corresponding
psf file. but I notice if I use vmd -psf prod.psf -pdb prod.pdb to see the structure, It is obvious that there is some problem of the bond of
ILE1, some bonds are broken, and if I use vmd -pdb prod.pdb to open it, it looks good. so it should be the problem of the psf file.
cound anyone tell me what 's the problem of the script.

# PSFGEN script to generate PSF from split up PDB file
package require psfgen

topology "top_mod.rtf"

segment PROD {
?first ACE
?last CT2
?pdb m1_prod_ADTaddH.pdb_charmm
pdbalias atom ILE CD1 CD
coordpdb m1_prod_ADTaddH.pdb_charmm PROD


patch DISU PROD:2 PROD:12

writepdb prod.pdb
writepsf prod.psf



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