[gmx-users] splitting chains

[Alpay Temiz]

Specbond.dat is used to construct the topology, Ozge. so it is used by pdb2gmx program.
Alpay


Message: 6
Date: Sat, 31 Mar 2007 00:36:14 +0200
From: Erik Marklund <erikm at xray.bmc.uu.se>
Subject: Re: [gmx-users] splitting chains
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <E2CEA1A6-0438-4D88-A3A1-6589ADEF5D53 at xray.bmc.uu.se>
Content-Type: text/plain; charset="iso-8859-1"


30 mar 2007 kl. 22.32 skrev özge kül:

> Hi Eric,
>
> Where  is the specbond.dat?After which line is it formed?

specbond.dat is located in <install directory>/share/gromacs/top/
I don't understand the question about the line.

/Erik

>
> 1.      pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o
> 1ppbfree.gro   -merge
> 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron
> 3.      genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro
> 4.      grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o
> 1ppbfree-en.tpr -p 1ppbfree.top
> 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-
> aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr
> Please help me?:)
>
> özge
>
> Bored stiff? Loosen up...
> Download and play hundreds of games for free on Yahoo! Games.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys


-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20070331/d17b33c5/attachment.html

------------------------------

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!

End of gmx-users Digest, Vol 35, Issue 99
*****************************************