On 7/16/14, 1:42 AM, Sarath Kumar Baskaran wrote:
Dear all, I was using PRODRG for my protein ligand Simulations, Later, I came across the issues of PRODRG topologies on atom charges, and i have been tryiing to correct these problems. I couldnt use ATB since it gives topopology only for GROMOS96 53a5 and 53a6 force field whereas i need for GROMOS96 43a1. There is a program - ITP Adjuster, an utiltity to correct these charges. Journal of Chemistry - Volume 2013 (2013), Article ID 803151, 6 pages ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server. http://dx.doi.org/10.1155/2013/803151 **Is it wise to use this program to correct the PRODRG output ?
Looking briefly through that paper, it seems that the charges are somewhat over-fitted, and in some cases very different from the existing functional groups in the force field. The "validation" they provide simply states that their program changed the charges; it doesn't demonstrate that the topologies are sane.
QM calculations are the first, but not final, step in deriving Gromos-compatible topologies. You can piece together most molecules from existing functional groups; transferability is at the heart of any force field, particularly one built in pieces as the Gromos parameter sets have been.
-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.