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.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
