Hi,
15 okt 2009 kl. 07.08 skrev [email protected]:
The reason I am asking this is because it will require me to create
gromacs compatible FF files of the Charmm FF . I did find two perl
scripts which can do probably handle that but i am wondering if the
compatible FF are already up on gromacs website somewhere.
No, it is not available on the gromacs website yet. You can get the
current parameter files from me if you'd like to try it out. I'm
afraid the DPPC lipid in CHARMM is created by combining the PALM and
PCGL residues and some patches so if you know how that works in CHARMM
you might be able to create the DPPC residue.
No one ever said life was easy :) CHARMM support is under
development, you can
get the source via the git repositories, but I don't know its
current status.
As Justin is saying, CHARMM will be supported as of version 4.1. The
source code is there in git master branch but you need to get the ff
files from me.
I have been trying to search for an all atom DPPC sructure
(including the missing Hydrogens of long chain hydrocarbons) and
then do an all atoms md simulation on it. I havent yet found any
such structure or any force field that could be used for it on the
internet. Is anybody familiar with any such work ?
Is there any all atom model for hydrocarbons which is incorporated
in Gromacs? I am not 100 % sure about it.
I want to do this to parametrize another force field which
essentially uses all atom model.
/Pär Bjelkmar
<><><><><><><><><><><><><><><><><><>
Pär Bjelkmar, PhD student
Stockholm Center for Biomembrane Research,
Stockholm Bioinformatics Center,
Department of Biochemistry and Biophysics,
Stockholm University
Tel: +46-8-16 2746
Fax: +46-8-15 3679
E-mail: [email protected]
Home: http://www.dbb.su.se/User:Bjelkmar
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