>> When running grompp, yes, the order is significant and the coordinates must match the topology.
am little confused about 'coordinates'. Say if I have two structures which are well equlibrated and just represent two different configurations and also the atom order matches with some common top file then even I can not use same .top file? On Tue, Feb 4, 2014 at 5:39 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/4/14, 12:35 PM, gromacs query wrote: > >> Hi Justin >> >> Presence of the correct atoms is the only absolute requirement >>>> >>> >> Thanks. Correct 'atoms' mean correct 'atom names'? so does that mean I >> should rename my atoms according to rtp file? >> >> > Yes, atom names need to match. That's all that's in a coordinate file, > anyway. > > > Also one more question: I think atom order does matter when I load a pdb >> and use some .top file? (and if I understood it correctly; if I am using >> from rtp file, which is a sort of residue library file, then order does >> NOT >> matter) >> >> > When running grompp, yes, the order is significant and the coordinates > must match the topology. That is because bonded geometry, exclusions, etc. > are based on atom numbers, which follow a specific order. pdb2gmx is a bit > smarter (surprisingly) in terms of sorting out the atoms it finds, but at > the point that it loads the .rtp and checks the input coordinate file, all > it is doing is making sure all the atoms it needs are present. Bonds and > things are assigned later. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > 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. > -- 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.