[gmx-users] ffG43a2x and ffgmx dppc.itp file

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 5 15:47:03 CEST 2006

P wrote:
> Dear All
> I have question for  people who use dppc lipids with ffG43a2x.tgz force 
> field
> (GROMOS96 modified to describe lipids).  I want to change to newer GROMOS96
> force field (in order to simulate membrane/protein water systems) and I 
> would
> 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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