[gmx-users] itp to top(moose.bio.ucalgary.ca)

Itamar Kass ikass at cc.huji.ac.il
Tue Jul 29 21:15:01 CEST 2003

Quoting Osmany Guirola Cruz <osmany.guirola at cigb.edu.cu>:

> in the site http://moose.bio.ucalgary.ca i find PDB bilayers and ITP files
> whit editconf i have the gro file but not the top file
> when i use pdb2gmx , i obtain MANY warnings
> i need to know how to convert the itp file to a top file
> What should i do?
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   Hi Osmany, I can give you the answer I got from Bert de Groot when I asked
the same qustion:

you don't need pdb2gmx for the lipids. Just include the ffgmx.itp from the
ffgmx_lipids.tar.gz (which also defines the params from lipid.itp, so that
you don't need to include lipid.itp anymore). Then include dmpc.itp and you're
ready to run.

your topology could look something like this:

#include "./ffgmx.itp"
#include "dmpc.itp"

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

[ system ]
; Name
DMPC in water

[ molecules ]
; Compound        #mols
DMPC    271
SOL    4238

Computers are like airconditioners... They don't work well with Windows

| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Group Homepage: http://www.ls.huji.ac.il/~membranelab/

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