[gmx-users] RE. pdb2gmx with force field option (Mohamed Osman)

[Kia Balali-Mood]

jagshemash (hi) Mohammed,
OK there are two ways of dealing with this:

1. You add water with genbox ....run grommpp ..then feed in the resulting *tpr
file into genion...genion replaces a water molecule with a pre-selected
appropriate ion ("genion -h" should give you the help menu). However, you must
remember to #include ions.itp in your *top file.

If for some reason you don't want water in your system
2. You just manually put a K+ ion in yourself but need to define it in your own itp

something like this should do..if u copy it into a ascii file.

[ moleculetype ]
; name  nrexcl
K      1

[ atoms ]
; id    atype   resnr   resname aname   cgnr    charge          mass    
    1   K+     1       K      K      0        1.000          22.9898

cheers
Kia

> 
> Message: 3
> Date: Thu, 9 Nov 2006 11:55:57 -0600
> From: "Mohamed Osman" <osmangmx at gmail.com>
> Subject: [gmx-users] pdb2gmx with force field option
> To: gmx-users at gromacs.org
> Message-ID:
> 	<5de0a28d0611090955s47976acdl9c89dd0139d8bb1c at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 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.itpfile, 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?
> 
> 
> Thanks
> 
> Mohamed Osman
> Professor of Electrical Engineering
> Washington State University


-- 
Kia Balali-Mood PhD, CBiol, MIBiol
Postdoctoral Research Associate, Department of Biochemistry, 
Oxford University, OX1 3QU, UK
sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275)