On 5/6/14, 5:18 AM, Balasubramanian Suriyanarayanan wrote:
Dear all In membrane protein simulation do we need to treat the Protein with lipid model with Leap module of AMBER before pdb2gmx step. what is the point in
No idea what this means.
giving "none" option in response to -ter command. where we have capped N and C termini before pdb2gmx command? Please clarify.
Normal termini in Gromacs are built based on the assumption that a polypeptide chain has free amine and carboxyl groups at the respective termini, so pdb2gmx acts accordingly to build whatever H and O atoms are needed. In the case of capping groups, no such manipulation should be applied, hence you choose "None" to signify that no changes should be made to the atoms present.
-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 jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org.
