On 8/11/15 10:15 PM, Vy Phan wrote:
Dear Dr. Justin and Gromacs User, Thank you so much for your helps. When I use charmm36 ff to generate the topology for lipid (DOPC). I got many warning "Warning :Long bond " And after get the topology, the total charge is very high (+888 e for DOPC bilayer have 516 molecular). When I used grompp to generate the .tpr file, I got the many error like this : Error 3379 [file topol_Other_chain_D.itp, line 198252] No defaut U-B types ... Error 2379 [file topol_Other_chain_D.itp, line 98252] No default Proper Dih.type .... What can I do to modified the topology to get the correct charge and fix the error ? I download dopc.itp from Tieleman's website. I run simulation and all things look fine. People have experiences, please tell me the difference of this topology and the one on the charmm36 force field.
The files Tieleman provides are united-atom structures that may use a different naming convention. They won't have H atoms on the aliphatic groups and there is no .hdb entry for DOPC. The ridiculous net charge you got for DOPC (which is neutral!) should be an indicator that whatever topology you built is utter nonsense. There should also be no warnings about missing parameters, so this is further evidence that the topology is wrong and the "things look fine" assertion seems totally unfounded to me.
If you want to simulate a simple membrane, use CHARMM-GUI to build it. It will be 100% CHARMM compliant and we give you all the necessary input files.
-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].
