[gmx-users] Re: Preparation of the pure lipid system with charmm force field

[Justin A. Lemkul]

James Starlight wrote:
> So I should to use topol.top obtained for 1 lipid as the lipid.itp for 
> the sustem contained of the same lipids, shouldnt I?
> 

A .top can be converted to a .itp which can then be included in a real system 
.top topology.  So the lipid .top that you receive from pdb2gmx should be 
modified according to:

http://www.gromacs.org/Documentation/File_Formats/.itp_File

-Justin

> 2011/10/21 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     James Starlight wrote:
> 
>         Justin,
> 
>         In that way there was only one point wich was not understood for me
> 
> 
>         In charmm I already have lipids.rtp with the parametries for my
>         lipids. Also I have a single molecule of my lipid.
>         How via pdb2gmx I could create parametrised itp file except of
>         posre.itp ?
> 
> 
>     If you don't need posre.itp, don't use it.  What you really need is
>     the topology for the lipid, which pdb2gmx will write for you,
>     provided the input is syntactically correct and in agreement with
>     the .rtp file.
> 
>     -Justin
> 
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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-- 
========================================

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

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