[gmx-users] Re: Hi

[Justin A. Lemkul]

Please keep correspondence on the gmx-users listserv, so that an archived copy
will be preserved for others to benefit from later.  See my replies below.

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Hi Mr. Justin,
> Sorry for the posting my question to your personal mail,
> You made me clear so many doubts in gromacs , Thanks for that. But I have
> one doubt since one week trying get answer by different ways, but I didn't
> find, that is FF for protein in POPC. you replied me that read literature I
> read it. I found that using united atom FF( Berger) for lipid and all atom
> FF(OPLS) for protein, in case of membrane protein simulation,i tried to use
> in this way but it showing error, when I do minimisation
> I mentioned  FF in .top in this way,

Well, what is the error?  It is of no use to say that something didn't work. 
What were you doing?  What was the *exact* command you issued?  What was the
*exact* error message?

>
> Include forcefield parameters
> #include "ffoplsaa.itp"   - for protein
> #include "ffgmx.itp        -  for lipid
> #include "lipid.itp"
> #include "popc.itp"

Right; this is a problem.  Inclusion of both ffoplsaa.itp and ffgmx.itp will
probably cause the two to fight.  If you look through the list archives
thoroughly, you will find an excellent procedure written by Chris Neale related
to exactly how to do this.  You may also want to refer to Chapter 5 of the
manual for general information on topologies.

> Pls give me detail explanation  and suggest, normally which FFs use when
> protein inserted into POPC

Refer to the literature.  I have seen papers that have used Gromos96 and OPLS-AA
for membrane protein simulations.  The choice is up to you, based on what you
find and what you believe to be most applicable to your system.

-Justin

> Thanks in advance.
>



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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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