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:
http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
I have also a script that does automatize it completely, but it it not
for all purpose actually, so i'll share it later.
Cheers,
Stéphane
--
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
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