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.
