<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><BR><BR>--- On <B>Wed, 3/11/09, Adrien Delmont <I><adriendelmont@yahoo.com></I></B> wrote:<BR>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">From: Adrien Delmont <adriendelmont@yahoo.com><BR>Subject: Re: [gmx-users] get a box of 100 molecules<BR>To: jalemkul@vt.edu<BR>Date: Wednesday, March 11, 2009, 9:46 PM<BR><BR>
<DIV id=yiv2096492447>
<TABLE cellSpacing=0 cellPadding=0 border=0>
<TBODY>
<TR>
<TD vAlign=top>
<DIV>The molecule I use is a simple hydrocarbon ( n-heptane ) and I think that I should add something like dihedral, bond, angle parameters after I search the literature. I found some information about that. I think I will add parameters into the related force fields .itp file. Is it true ? And then I will create a box of 100 molecules without any error.<BR><BR>--- On <B>Wed, 3/11/09, Justin A. Lemkul <I><jalemkul@vt.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid">From: Justin A. Lemkul <jalemkul@vt.edu><BR>Subject: Re: [gmx-users] get a box of 100 molecules<BR>To: adriendelmont@yahoo..com, "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Wednesday, March 11, 2009, 9:11 PM<BR><BR><PRE>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@anu.edu.au>/*
wrote:
>
> From: Mark Abraham <Mark.Abraham@anu.edu.au>
> Subject: Re: [gmx-users] get a box of 100 molecules
> To: "Discussion list for GROMACS users"
<gmx-users@gromacs.org>
> Date: Wednesday, March 11, 2009, 4:58 PM
>
> Adrien Delmont wrote:
> > > >
------------------------------------------------------------------------
> > *From:* Adrien Delmont <adriendelmont@yahoo.com>
> > *To:* jalemkul@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@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@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users@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@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
========================================
</PRE></BLOCKQUOTE></TD></TR></TBODY></TABLE><BR></DIV></BLOCKQUOTE></td></tr></table><br>