[gmx-users] help with lipids and pdb2gmx

[Justin A. Lemkul]

Quoting fabracht sdf <fabracht at gmail.com>:

> Hi, I've downloaded all the force field itps and extra ipt files necessary
> for a popc bilayer simulation. They are all in my top directory, but i
> haven't figured out how to use this with pdb2gmx in order to generate my
> topology files. I would appreciate, if possible, some help on the subject.
> Thank you in advance
> Fabrício Bracht
>

The short answer: you don't use pdb2gmx for lipids.  One would only use pdb2gmx
with proteins/nucleic acids (and a small assortment of other molecules) that
are present in the .rtp entry for a given force field.  You cannot use .itp
files as input into pdb2gmx.   A thorough read of Chapter 5 in the manual will
tell you how to include topologies of special molecules, like lipids.

Do a thorough search of the list archive for this issue; it has been discussed
dozens of times, and there are very useful descriptions of exactly what to do. 
Look for posts by Chris Neale; his procedure is quite clear.

-Justin


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Justin A. Lemkul
Graduate Research Assistant
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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