Re: [gmx-users] pdb2gmx with force field option

[Stéphane Téletchéa]

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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Re: [gmx-users] pdb2gmx with force field option

[Mark Abraham]

 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?

No that won't work. You need to choose a force field that has been
parameterized to include your protein and your ion. I don't know if this
one has.

 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?

You can use the #include mechanism in your .top if you have an .itp file
for potassium.

 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.itpfile, is that enough?

Yes, if it's complete. Have a read of chapter five of the manual.

 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?

Start with MD on a simple system while you work out how things work. First
just your protein. Then with the ion. Then worry about the lipid.

 4. What is a better way of doing step 3?

I don't know.

Mark

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