please excuse me sir
On Mon, 3 Sep 2018 22:59 Justin Lemkul, <jalem...@vt.edu> wrote: > > > On 9/3/18 2:28 PM, Mahdi Sobati Nezhad wrote: > > how can I build hydrogens own, after -ignh command?! > > Please re-read what I just said. > > -Justin > > > On Mon, 3 Sep 2018 22:55 Justin Lemkul, <jalem...@vt.edu> wrote: > > > >> > >> On 9/3/18 2:24 PM, Mahdi Sobati Nezhad wrote: > >>> Yes. Now my problem is HG in residue CYS that I don't know rename to > >> what!!! > >> > >> Either the names in the PDB file need to be made consistent with what is > >> in the .rtp file, or you should use -ignh to have pdb2gmx ignore all > >> input H atoms and build its own, all of which will be properly named. > >> > >> -Justin > >> > >>> On Mon, 3 Sep 2018 22:49 Justin Lemkul, <jalem...@vt.edu> wrote: > >>> > >>>> On 9/3/18 6:27 AM, Mahdi Sobati Nezhad wrote: > >>>>> Hi > >>>>> my pdb file named HB2 and HB3 but .rtp file in my force field named > >>>> HB1and > >>>>> HB2. and so on error "atom HB3 in residue xxx was not found in rtp > >> entry" > >>>>> can I rename HB2 to HB1 and HB3 to HB2 ? > >>>>> or any idea?! > >>>> Have you tried it? > >>>> > >>>> -Justin > >>>> > >>>> -- > >>>> ================================================== > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Virginia Tech Department of Biochemistry > >>>> > >>>> 303 Engel Hall > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> jalem...@vt.edu | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> ================================================== > >>>> > >>>> -- > >>>> 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. > >> Assistant Professor > >> Virginia Tech Department of Biochemistry > >> > >> 303 Engel Hall > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> 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. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.
