[gmx-users] get a box of 100 molecules

[Justin A. Lemkul]

Adrien Delmont wrote:
>  
> I just want to add missing parameters for my molecule in order to get 
> ..gro and top files for example GROMOS96 43a2 force field . How can I 
> add missing parameters ? I didn't find any information about this 
> procedure. I'm waiting for your help.
>  

You'll have to define what you mean by "parameters" - is this some new small 
molecule that has not been parameterized under this force field?  Are you 
starting from scratch?  If so, this is not a trivial problem for a beginner. 
Read here:

http://wiki.gromacs.org/index.php/Parameterization

If you have adequate parameters for most of your molecule and are missing 
something like a dihedral, etc. then read the primary literature and derive it 
yourself.  This process is also complicated, but is probably less work than 
coming up with parameters for a brand new molecule.

-Justin

> Thanks in advance
> 
> 
> --- On *Wed, 3/11/09, Mark Abraham /<Mark.Abraham at anu.edu.au>/* wrote:
> 
>     From: Mark Abraham <Mark.Abraham at anu.edu.au>
>     Subject: Re: [gmx-users] get a box of 100 molecules
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Wednesday, March 11, 2009, 4:58 PM
> 
>     Adrien Delmont wrote:
>     > 
>     > 
>     > ------------------------------------------------------------------------
>     > *From:* Adrien Delmont <adriendelmont at yahoo.com>
>     > *To:* jalemkul at vt.edu
>     > *Sent:* Wednesday, March 11, 2009 6:09:53 PM
>     > *Subject:* Re: [gmx-users] get a box of 100 molecules
>     > 
>     > I didn't get gro and top files with any force field in Gromacs. I
>     basicly want to use oplsaa and GROMOS96 43a2 force field (improved alkane
>     dihedrals) . I think I should add all the parameters but  how can I add my
>     parametes both into oplsaa and GROMOS96 43a2 force field ?
> 
>     You can't just mix force fields. See
>     http://wiki.gromacs.org/index.php/force_field
> 
>     Mark
>     _______________________________________________
>     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
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> 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

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================