Hi, Files in fixed-column formats use the column widths to separate elements. They don't use white space at the same time, for the same job! Try it and see ;-)
Mark On 26/04/2015 6:29 am, "Brett" <brettliu...@163.com> wrote: > Dear All, > > If we change HIS188 in Chain B to HISE188 in Chain B, before change the > PDB looks like > "HIS B 188", but after change the PDB will look like "HISEB 188", which > makes thereis no space between "HISE" and "Bchain". I do not know whether > pdb2gmx can recognize HISEB 188, or we process it in some other way. > > I am looking forward to getting a reply from you. > > Brett > > > > > > > > > At 2015-04-26 11:08:19, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > > > >On 4/25/15 11:05 PM, Brett wrote: > >> Dear All, > >> > >> For gromacs, for HIS residues there are HISD,HISE and HISH. In the > original PDB file, are HIS residues are written as HIS. If based on > necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS > to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling > with all the other coordinate lines. Does pdb2gmx recognize these > non-aligned coordinate lines? Or what other strategy you recommend me to > take so that pdb2gmx can recognize HISD,HISE and HISH? > >> > > > >Do the replacement properly and don't screw up column alignment. It > needs to be > >correct for proper interpretation of the coordinates. > > > >-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.