Hi Par Bjelkmar, I need to do an all atom simulation for dppc bilayer . You are right the dppc molecule file that i have has PALM and PCGL residues.
I will like to try to set up the charmm FF for gromacs. But I dont have the FF files with me, neither do i have the programs. Could you send me a tutorial or some reference link too ( if you know of any). Thank you, Amit On Thu, Oct 15, 2009 at 4:01 AM, Pär Bjelkmar <[email protected]> wrote: > 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 > > <><><><><><><><><><><><><><><><><><> > > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 >
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