[gmx-users] fatal error [using pdb2gmx]
mdsimulation at hotmail.com
Sun Oct 16 23:31:35 CEST 2005
thak you for replying. If I want to write my own .pdb file how can I get the
configuration for it?
I have a paper talking about the bond length and angles in the Glycine. how
can I use this information to write my own .pdb file?
>From: Tsjerk Wassenaar <tsjerkw at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] fatal error [using pdb2gmx]
>Date: Sun, 16 Oct 2005 20:09:49 +0100
>The pdb file contains all hydrogens, while you chose a united-atom force
>field probably. Use the option -ignh.
>On 10/16/05, Sven Huttenhouse <mdsimulation at hotmail.com> wrote:
> > dear GROMACS users.
> > I'm a new gromacs user from Illinois Institute of Technology (IIT).
> > I'm trying to get the pdb file of Glycine to study glycine
> > crystallization.
> > I found an online pdb file for it. but when I used pdb2gmx to convert it
> > to
> > a .gro file I got the following error message:
> > fatal error: atom H9 in risidue GLY 1 not found in rtp enrty with 7
> > while sorting atoms. maybe different protonation state. remove this
> > hydrogen
> > or chose a different protonation state.
> > option -ignh will ignore all hydrogen in the input.
> > I got the glycine pdb file from the following link
> > http://wbiomed.curtin.edu.au/teach/biochem/tutorials/pdb/
> > can any one help me please. and is there any other way to construct my
> > .pdb
> > file for any molecule.
> > kind regards
> > Sven Huttenhouse.
> > _________________________________________________________________
> > Don't just search. Find. Check out the new MSN Search!
> > http://search.msn.click-url.com/go/onm00200636ave/direct/01/
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
>Tsjerk A. Wassenaar, M.Sc.
>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
>Dept. of Biophysical Chemistry
>University of Groningen
>9747AG Groningen, The Netherlands
>+31 50 363 4336
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
Is your PC infected? Get a FREE online computer virus scan from McAfee®
More information about the gromacs.org_gmx-users