Thanks, I reused DMPC layers from CHARMM-GUI after some editing.I was able to pin-down issue here, test file:http://www.mediafire.com/file/usuv55c3j505ec2/test.pdbI can do:gmx pdb2gmx -f test.pdb -o test.gro -water spce Without error. But if I do:gmx pdb2gmx -f test.pdb -o test.gro -water spce -ignhI get error about hydrogen which I try to ignore. Very strange for me. -ignh option is not possible with CHARMM ff?
On Tuesday, April 4, 2017 3:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 4/4/17 8:52 AM, Vytautas Rakeviius wrote: > Hello, > I have my system with DMPC bilayers in pdb and try to convert it into GROMACS > input. Because system is with lipids I think chose CHARMM27 ff. But still I > get lots of warnings like that: > > https://pastebin.com/K8dHKkUi > Also I add my DMPC pdb as example. What should I do? Rename all my DMPC > atoms?Thanks for all suggestions. > > This is the same with any force field; the atom names have to match the force field's expectations. If you're just trying to build a DMPC bilayer, construct one using CHARMM-GUI. It's guaranteed to have CHARMM-compliant nomenclature (and you should be using CHARMM36 for lipids, anyway, because the CHARMM27 parameters are not nearly as good for lipids). -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 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.