VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Tue Mar 02 2010 - 11:17:42 CST

you're right, the termini are screwed up.
for nucleic acids you have to specify roper termini, i.e. sth like
FIRS 5TER
LAST 3TER

Your question concerning the manual: check
http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/
there is a ling to a user's guide

eddie

On Mar 2, 2010, at 10:50 AM, YangMingjun wrote:

> Dear all,
> I am going to create a psf file for the protein-RNA complex by
> psfgen. But output message manifested something wrong.
> The input file I used is:
> ---- psf.tcl
> # (1) Split input PDB file into segments}
> # (2) Embed the psfgen commands in this script
> psfgen << ENDMOL
> # (3) Read topology file
> topology top_all27_prot_na.rtf
> # (A) Build protein segment
> segment A {
> pdb protein-min-a.pdb
> }
> # (A) Read protein coordinates from PDB file
> coordpdb protein-min-a.pdb A
> ############################
> # (A) Build protein segment
> segment B {
> pdb rna-min-b.pdb
> }
> # (A) Read protein coordinates from PDB file
> coordpdb rna-min-b.pdb B
>
>
> writepsf system.psf
> writepdb system.pdb
> # End of psfgen commands
> ENDMOL
> ---------
>
>
> Part of the output is:
> -------
> ...
> building segment B
> reading residues from pdb file rna-min-b.pdb
> extracted 47 residues from pdb file
> Info: generating structure...
> Info: skipping conformation O3'-O5'-P-O2P at beginning of segment.
> Info: skipping conformation O3'-O5'-P-O1P at beginning of segment.
> Info: skipping conformation O3'-P-O5'-C5' at beginning of segment.
> Info: skipping bond O3'-P at end of segment.
> Info: skipping conformation C3'-O3'-P-O5' at end of segment.
> Info: skipping conformation C4'-C3'-O3'-P at end of segment.
> no atom C in residue GUA:1 of segment B
> Warning: add conformation failed in patch NTER
> B:1
> no atom CA in residue CYT:47 of segment B
> Warning: add improper failed in patch CTER
> no atom CA in residue CYT:47 of segment B
> Warning: add conformation failed in patch CTER
> no atom N in residue CYT:47 of segment B
> Warning: add conformation failed in patch CTER
> B:47
> Info: segment complete.
> reading coordinates from pdb file rna-min-b.pdb for segment B
> Warning: failed to set coordinate for atom H5T GUA:1 B
> Warning: failed to set coordinate for atom H3T CYT:47 B
> Info: writing psf file system.psf
> ...
> ------
>
> It seems that there is something wrong with the 3' and 5' terminal
> ends of the RNA segment.
> Could someone please tell me how to fix this problem?
>
> Another question is where to find the manual for psfgen?
>
> Thanks for the time.
>
>
> Yang Mingjun
>
> 2010-03-03
>
> -----------------------------------------------
> State Key Lab of Molecular Reaction Dynamics (SKLMRD),
> Dalian Institute of Chemical Physics(DICP),
> the Chinese Academy of Sciences(CAS),
>
> Zhongshan Road457, Dalian City,
> Liaoning Province 116023,P. R. China
>

=====================================================
Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078
http://www.ks.uiuc.edu/~eschrein/
=============================================