[gmx-users] pdb2gmx with force field option

Stéphane Téletchéa steletch at jouy.inra.fr
Fri Nov 10 13:42:21 CET 2006

Mohamed Osman a écrit :
> As my first Gromacs simulation I am trying to simulate a protein with K+ 
> ion. 
> When I use pdb2gmx with GROMACS96 43a2, it complains about the K+ ion 
> and does not generate the topology file.
> When I remove the K+ ion, I get a topology file, but I need the K+ for 
> the simulation.  Can I add the K+ ions at the end of the .gro files and 
> proceed?
> 1. How can I run pdb2gmx and tell it to look for the force filed 
> information for K in a different file?  I tried -ff but got unclear message?
> 2.  When I searched in the share/top directrory I found that each force 
> field name with several extensions:.itp, .dhb and .atp.  I only have a 
> K.itp file, is that enough?
> 3.  To insert the protein into a lipid I used genbox command:
>      genbox -cp protein.pdb -cs lipid.pdb
> The protein sinks deep into the lipid and I need to shift the protein 
> back up? What is the best to do it without overlapping with the solvent 
> molecules?
> 4. What is a better way of doing step 3?

You should have a look at this paper: (it helped me a lot)
C. Kandt, W.L. Ash, D.P. Tieleman. Setting up and running membrane 
protein simulations, Methods, in press

and use inflategro for doing it:

I have also a script that does automatize it completely, but it it not 
for all purpose actually, so i'll share it later.



Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

More information about the gromacs.org_gmx-users mailing list