hello gromacs users ohk justin but if unk is deleted then how to put it back in system_inflate.gro
On Wed, Jul 9, 2014 at 5:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/9/14, 6:17 AM, RINU KHATTRI wrote: > >> hello every one >> I am working on complex with popc membrane i did >> >> perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat >> >> after this step minimization >> >> grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr >> >> i got error >> Fatal error: >> number of coordinates in coordinate file (system_inflated.gro, 10224) >> does not match topology (topol.top, 10245) >> i have been removed 6 lipid molecules in my topology file according to >> output i got one thing new in my system_inflate.gro file the written >> displayed atom is 10224 but after counting it is 10536 so if i correct it >> difference is more >> > > I don't know what this means, but the number of atoms that grompp is > finding is going to be correct. > > > in topology file [molecule] >> protein chain 1 >> UNK 1 >> POPC 122 >> how to resolve it >> > > I would venture a guess that UNK has 21 atoms. I don't know that > InflateGRO handles arbitrary molecules, so it may have gotten deleted upon > inflation. Check system_inflated.gro; it will be very obvious if it is > missing. > > -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. > -- 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.