[gmx-users] Pdb for urea crystal

[Tsjerk Wassenaar]

Hi,

Please do follow the tutorial:

http://md.chem.rug.nl/education/mdcourse/index.html

and read the Gromacs manual. Try to understand each step in setting up
and running a simulation, including the formats for all the (human
readable) files used/produced at each step.

Sincerely,

Tsjerk

On 11/1/06, merc mertens <merc.mertens at gmx.net> wrote:
> hello,
>
> your gro contains 8 urea molecules and your top only one. you should change the line " UREA             1" in your "[ molecules ]"-section to " UREA             8".
>
> merc
>
>
> -------- Original-Nachricht --------
> Datum: Wed, 1 Nov 2006 17:46:59 +0800
> Von: "Sivashangari Gnanasambandam" <g0501135 at nus.edu.sg>
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] Pdb for urea crystal
>
> > Hi,
> >
> >
> >  <<one.gro>>  <<one.pdb>>  <<one.top>>
> > I am very new to the GROMACS and I couldn't able to proceed further from
> > converting a pdb file to gro file for one month.
> >
> > I tried to create topology file using the format suggested in mailing
> > list but it shows the error '' No of coordinates in gro file does not
> > match with topology'. I attached my gro and top file for your reference.
> > Kindly help me to come out from my problem.
> >
> >
> > Thank you
> > Shankari
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336