These are lines that cause trouble: ERROR 1 [file mCherry7.top, line 18183]: No default U-B types
ERROR 2 [file mCherry7.top, line 18250]: No default U-B types ERROR 3 [file mCherry7.top, line 25379]: No default Proper Dih. types ERROR 4 [file mCherry7.top, line 25380]: No default Proper Dih. types ERROR 5 [file mCherry7.top, line 25383]: No default Proper Dih. types ERROR 6 [file mCherry7.top, line 25386]: No default Proper Dih. types ERROR 7 [file mCherry7.top, line 25387]: No default Proper Dih. types ERROR 8 [file mCherry7.top, line 25388]: No default Proper Dih. types ERROR 9 [file mCherry7.top, line 25455]: No default Proper Dih. types ERROR 10 [file mCherry7.top, line 25457]: No default Proper Dih. types ERROR 11 [file mCherry7.top, line 25458]: No default Proper Dih. types Now in these files which I have already uploaded I have only added two extra lines just above [ angles ] section of CH6 residue in aminoacids.rtp (lines 1793 and 1794): MC3 +N 0.1345 154808.0 MN1 -C 0.139 173594.2 I have not changed anything else in any other file. Now the problem is that I have consecutive residues Phe65-CH6-Ser69. MN1 atom of CH6 is supposed to be bonded to C atom of Phe65. MC3 atom of CH6 is supposed to be bonded to atom NH1 of Ser69. C atom of Phe65 is not supposed to be bonded to NH1 atom of Ser69 but it is in my *top file. What other files do you need? Best wishes, Dawid Grabarek 2014-08-06 20:04 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 8/6/14, 12:52 PM, Dawid das wrote: > >> Yes CH6 is defined as a Protein. In fact pdb2gmx sees two chains. How to >> work it out then? >> >> > You'll need to provide files and describe exactly what the problems are > (lines in the topology, please) and what changes you have made since the > last bundle of files you uploaded. > > -Justin > > > >> 2014-08-06 19:45 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 8/6/14, 12:04 PM, Dawid das wrote: >>> >>> Cause now what happens is that grompp requires bonding parameters for >>>> atoms >>>> which are actually bonded and for which are not (angle and dihedral >>>> parameters), e.g. CH6-Ser69 and CH6-Phe65 is what I want but I do not >>>> want >>>> connection between Ser69-Phe65. Now grompp asks me about bonding >>>> paramters >>>> for atoms which build all three residues while these residues are >>>> separated >>>> by more than 4 atoms. >>>> >>>> >>>> Properly constructed .rtp entries will not need manual editing, which >>> is >>> very error-prone. You're using lots of strange atom names, so you need >>> to >>> establish proper bonding from the CH6 residue; the +/- mechanism in >>> flanking residues will fail. If you're getting connections between >>> non-consecutive residues, that suggests a break in the chain when being >>> processed by pdb2gmx; make sure CH6 is defined as a Protein residue in >>> residuetypes.dat. >>> >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA 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 >>> >>> 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. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA 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 > > 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.