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 <jalem...@vt.edu <mailto:jalem...@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
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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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
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