[gmx-users] question about all atoms lipid molecule
bjelkmar at cbr.su.se
Thu Oct 15 13:01:36 CEST 2009
15 okt 2009 kl. 07.08 skrev gmx-users-request at gromacs.org:
>> 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, PhD student
Stockholm Center for Biomembrane Research,
Stockholm Bioinformatics Center,
Department of Biochemistry and Biophysics,
Tel: +46-8-16 2746
Fax: +46-8-15 3679
E-mail: bjelkmar at cbr.su.se
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