Hi, Please do everyone the courtesy of starting a new email, rather than replying to a digest and confusing the archive and email readers.
On Thu, Apr 30, 2015 at 3:50 PM Ming Tang <m21.t...@qut.edu.au> wrote: > Hiļ¼Justin > > I have been told by an author of one journsl that pdb2gmx can convert PRO > to HYP while generating. I did not find the option. Can you give me some > advice. > Get knowledgeable reviewers ;-) You can't do it with pdb2gmx. Some building programs are suggested on the GROMACS website. Mark > Thanks > Sent from my Huawei Mobile > > Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 4/30/15 6:46 AM, vidhya sankar wrote: > > Dear justin Thank you for you reply > > > > Also when i use g_enemat tool as follows > > > > > > g_enemat_d -f CNTPEPRSOLIONSfulllatest3.edr -groups group.dat -emat > jnnff.xpm > > > > it shows the following error > > Opened CNTPEPRSOLIONSfulllatest3.edr as single precision energy file > > Will read groupnames from inputfile > > Read 2 groups > > group 0WARNING! could not find group (null):CYCLIPEPTIDE1-CYCLIPEPTIDE1 > (0,0)in energy file > > WARNING! could not find group (null):CYCLIPEPTIDE1-CYCLIPEPTIDE2 (0,1)in > energy file > > group 1WARNING! could not find group (null):CYCLIPEPTIDE2-CYCLIPEPTIDE2 > (1,1)in energy file > > > > Will select half-matrix of energies with 6 elements > > Last energy frame read 25000 time 50000.000 > > Will build energy half-matrix of 2 groups, 6 elements, over 25001 frames > > Segmentation fault (core dumped) > > though i set > > 2 > > CYCLIPEPTIDE1 > > CYCLIPEPTIDE2as energy groups .my .mdp file whil running MD > > > > So why it shows error? > > > > A seg fault is usually a bug. There was a g_enemat seg fault in an old > version, > but it was fixed. If you're not using 5.0.4, you should be. > > -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. > -- > 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.