[gmx-users] Re: Preparation of the pure lipid system with charmm force field
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 21 15:24:50 CEST 2011
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:
> 2011/10/21 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> James Starlight wrote:
> 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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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