in fact Tyr363 is the C-terminus and the command is; pdb2gmx -f MARKII.pdb -o MARKII.gro -p MARKII.top I have TPO (phospho-threonie 208) as the non-standards amino-acid. so i used your introduced "gromos43a1p.ff" for pdb2gmx command.
On Saturday, January 25, 2014 11:04 PM, Justin Lemkul <[email protected]> wrote: On 1/25/14, 11:04 AM, Saman Shahriyari wrote: > dear Justin > thank you for answering. your instruction with "aminoacids.r2b file", helped. > this time i am having the following problem; > Program pdb2gmx, VERSION 4.6.3 > Source code file: /usr/local/Software/gromacs-4.6.3/src/kernel/pdb2gmx.c, > line: 727 > Fatal error: > Atom OXT in residue TYR 363 was not found in rtp entry TYR with 18 atoms > while sorting atoms. > > any suggestion on dealing with OXT? pdb2gmx thinks Tyr363 is the C-terminus. Is that correct? What is your exact command line? Do you have any nonstandard residues? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 ================================================== -- 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 [email protected]. -- 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 [email protected].
