[gmx-users] ffG43a2x and ffgmx dppc.itp file
Mark.Abraham at anu.edu.au
Wed Apr 5 15:47:03 CEST 2006
> Dear All
> I have question for people who use dppc lipids with ffG43a2x.tgz force
> (GROMOS96 modified to describe lipids). I want to change to newer GROMOS96
> force field (in order to simulate membrane/protein water systems) and I
> like to make *.itp file for dppc lipid molecule that is in agreement with
> ffG43a2x.tgz from the contribution section of gromacs website.
> ffG43a2x.tgz force field has two new atoms types LCH3 and LCH2 that can be
> used to describe long lipid chains. There are also new LJ parameters for
> those atoms in ffG43a2xnb.itp. What is the procedure for obtaining *itp
> for dppc molecule that can be used with this force field.
> 1) Should I use PRODRGbeta for creating dppc.itp topology and
> manually change atom types describing lipid long chains CH3 to LCH3 and
> then CH2 to LCH2.
That might work, so long as inappropriate numerical parameters don't get
embedded in the .itp file. I know nothing about PRODRG.
> 2) Should I download dppc.itp topology from gromacs benchmark
> and manually change the atom types to those present in ffG43a2x.
That might work, and would certainly be a good template if you wanted to
write your own.
> 3) Is there any available software that can be used for
> creation of dppc.itp file.
Not that I'm aware of. The manual has detailed descriptions of the .itp
file format, have a read of it.
> 4) .. is there a simpler way?
There can't be until someone comes up with a library of all known
molecules of interest. Even then, you would want to check the author's
assumptions carefully to see that you concur with their chemical judgement.
> Please give me some hints and suggestion,
> I’m not an expert with gromacs, what is the
> right procedure for this.
It's exacting work, but there is no avoiding it, unless someone has put
it in the Contributions section of the gromacs webpage.
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