[gmx-users] atom numbering
Dear Gromacs users, My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds). During preparation of topology and gro file, the residue number ordering is changed. Is there any possibility to preserve number ordering from pdb file during pdb2gmx transfer? Thank you in advance, Marta -- 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.
Re: [gmx-users] atom numbering
Justin already answered your question five days ago: Use the -norenum option for pdb2gmx Peter -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Marta Wisniewska Sent: Sunday, December 06, 2015 2:03 PM To: gmx-us...@gromacs.org Subject: [gmx-users] atom numbering Dear Gromacs users, My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds). During preparation of topology and gro file, the residue number ordering is changed. Is there any possibility to preserve number ordering from pdb file during pdb2gmx transfer? Thank you in advance, Marta -- 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.
Re: [gmx-users] atom numbering
On 12/1/15 7:38 AM, Marta Wisniewska wrote: Dear Gromacs users, My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds). During preparation of topology and gro file, the residue number ordering is changed. Is there any possibility to preserve number ordering from pdb file during pdb2gmx transfer? Use the -norenum option. -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.
[gmx-users] atom numbering
Dear Gromacs users, My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds). During preparation of topology and gro file, the residue number ordering is changed. Is there any possibility to preserve number ordering from pdb file during pdb2gmx transfer? Thank you in advance, Marta -- 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.
