On 3/17/14, 7:05 PM, dan42 wrote:
I am new to GROMACS. I am trying to use pdb2gmx to create a topology for PEG (O-C-C)n with only H on one terminal and OH on the other. I know that I need to add a residue entry to the forcefield for example to aminoacids.rtp in
Well, multiple residues actually, to account for terminal and repeating block residues.
http://www.gromacs.org/Documentation/How-tos/Polymers
the gromos54a7.ff folder. However, I do not know how to construct the residue entry. I do know the format but I do not know what values to enter for bonds, angles, dihedrals ect. Can anyone help me?
Parameters for alkanes are pretty much cut-and-paste from any residue that has CH2-CH2 linkages, in addition to the CH2-O-H groups at the ends. You can take the gb_*, ga_*, and gd_* parameters that you need based on what you find in ffbonded.itp - parameters are described in some detail there.
The problem you will have is the ether linkages. AFAIK there are no parameters for ethers in 54A7, though other related force field parameter sets (i.e., those for sugars) will have them. The Gromos parameter sets are all closely linked, so the parametrization protocol should yield reasonably compatible parameters. It's something you will want to check thoroughly.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
