On 1/15/15 1:58 PM, Jennifer Vo wrote:
Dear Justin, Thanks again! I have downloaded the topology from Automated Topology Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using the existing molecules. Checking all of the *.itp file with both GROMOS 54A7 and GROMOS 534A6 force field for all of the NADPH they provided, I see all of these have the "P,SI" type. I would like to ask for your advice in this case.
Sounds like an error to me. Distributing topologies that trigger fatal errors is probably not what they intended, so I suggest you make them aware of this problem. P and SI have the same nonbonded parameters, so you're safe to simply replace the "P,SI" with the proper atom type in this case.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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].
