[gmx-users] CHARMM lipids
bjelkmar at cbr.su.se
Fri Aug 27 13:20:49 CEST 2010
I send a copy of this discussion to gmx-users. We can continue the discussion there so other users can benefit from it.
27 aug 2010 kl. 09.27 skrev yuanyuan3201003:
> Dear professor,
> Thanks for your reply , but the lipid parameter in gromacs 4.5 beta2 is not including DPPC,DPPS ,DPPG , is there any method that I can get the parameter file ?
Ok - it's one of those lipids you're interested in.
Actually, we discussed this in gmx-developersa few days ago:
So, the conclusion is that there might be a way to include these residues as they are described in CHARMM (by building them from "patches") but that requires code changes in GROMACS in the line of what Roland suggests. This might or might not happen. If you want these lipids without having the time to wait for such a thing to be implemented, it should be rather straightforward to build these lipids (i.e. make new entries in the charmm27.ff/lipids.rtp file) by manual "gluing" together the individual constituents. For example, in the top file of the CHARMM ff (version c32b1), this information is given for building a DPPC:
!The following two residues (PALM and PCGL) and the two subsequent
!patches (EST1 and EST2) are a modular way to create DPPC.
!See the comments with EST1 and EST2 for more details. adm jr., Jul 99
> Thanks a lot ,
> Yuanyuan Wang
By the way I'm only a poor PhD student, no professor :)
Pär Bjelkmar, Ph.D. student
Stockholm Center for Biomembrane Research (CBR),
Stockholm Bioinformatics Center (SBC),
Department of Biochemistry and Biophysics (DBB),
Tel: +46-8-16 2746
Fax: +46-8-15 3679
E-mail: bjelkmar at cbr.su.se
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