Running through pdb2gmx as you said. With regards to having the original topology files, long story short, they are files from a half finished project of an ex-student. Files are missing and I am trying to resurect the work.
Thanks Anthony Dr Anthony Nash Department of Chemistry University College London ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 16 December 2014 15:18 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Renumber atom ids and charge group in topology (.itp) On 12/16/14 10:16 AM, Nash, Anthony wrote: > Hi Justin, > > If there isn't there isn't. I was just hoping to save myself the effort of > correcting for the missing atoms on the crystal structure and the conversion > of HIS to HIE/HID with the amber forcefield. > In theory, you can certainly write a converter to subtract N atoms from every atom number that is found in the topology, but that's a far bigger pain than just running through pdb2gmx again, in my mind. If you had a topology before, why are there missing atom and name issues? -Justin > Thanks > Anthony. > > Dr Anthony Nash > Department of Chemistry > University College London > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin > Lemkul [jalem...@vt.edu] > Sent: 16 December 2014 15:00 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Renumber atom ids and charge group in topology (.itp) > > On 12/16/14 9:54 AM, Nash, Anthony wrote: >> Dear gromacs users, >> >> Renumbering the atom ids in a .gro file is very straight forwards, however, >> after cutting out the first 1/2 of my protein I am having great difficulty >> aligning my .itp file upon running grompp. Till this stage, it has been far >> easier for me to remove one particular domain of my protein from my >> pre-existing .gro file than it would be to adjusting the original crystal >> structure .pdb file and go through the great pains of getting pdb2gmx to >> work. But unfortunately I am now left with the fatal error: >> >> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = >> 2720, while at->nr = 0) >> >> which is quite understandable. >> >> I discovered an .awk file on the gromacs website. It is approx 5 years old >> and fails to renumber my atoms in the .itp file correctly. It fails at [ >> angles ]. I've been 'googling' for a solution but I am yet to find one. >> > > If you're hacking off part of the protein, the most straightforward solution > is > to just regenerate a new topology with pdb2gmx. > > -Justin > >> All help is appreciated. >> Thanks >> Anthony >> >> Dr Anthony Nash >> Department of Chemistry >> University College London >> > > -- > ================================================== > > 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. > -- ================================================== 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.
