Re: about psfgen

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Sat Jul 04 2009 - 09:40:46 CDT

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

for reference:
http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf

hope it helps
Ramya

On Sat, Jul 4, 2009 at 8:59 AM, emilia.l.wu <emilia.l.wu_at_gmail.com> 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
>
> guesscoord
>
> patch DISU PROD:2 PROD:12
>
>
> writepdb prod.pdb
> writepsf prod.psf
>
> quit
>
> #ENDMOL
>
>

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