I realized my mistake :) Sorry. There was a few missing atoms and residues in the .pdb file. I had completed them using pymol and amber xleap tool. I hadnt used chain identifier while i added these missing atoms to the .pdb file. But the other all residues had a chain identifier in the .pdb file. So pdb2gmx's head was confused. But it works now.
And as you said before http://comments.gmane.org/gmane.science.biology.gromacs.user/62384 pdb2gmx dont need to the N and C prefixes in the 4.6.x series. I tested it. 2015-02-06 14:11 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 2/6/15 8:10 AM, Ahmet yıldırım wrote: > >> There isnt any breaks in chains. I checked it. But i use the middle domain >> of a structure. It means i deleted N-terminal and C-terminal domains. But >> it shouldnt be a problem? >> >> > Without seeing your full screen output and providing the PDB file for > download somewhere, there's no point in guessing. pdb2gmx finds a > zwitterionic, standalone lysine. Clearly there is a problem, otherwise > pdb2gmx wouldn't tell you there is one :) > > -Justin > > > 2015-02-06 14:04 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 2/6/15 8:03 AM, Ahmet yıldırım wrote: >>> >>> LYS is NOT termini residue. >>>> >>>> >>>> pdb2gmx thinks it is. Check your input coordinate file (and screen >>> output, which tells you where any breaks in chains occur). >>> >>> -Justin >>> >>> >>> 2015-02-06 14:01 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >>> >>>> >>>> >>>> >>>>> On 2/6/15 7:58 AM, Ahmet yıldırım wrote: >>>>> >>>>> 4 letter residue names of termini in pdb file are in the columns >>>>> 18-22. >>>>> >>>>>> I >>>>>> think they are correct columns? >>>>>> >>>>>> >>>>>> The problem, from the error message, is that you have a standalone >>>>>> LYS >>>>>> >>>>> (a >>>>> zwitterion), so it is (in a sense) both NLYS and CLYS. The Amber force >>>>> fields (as implemented) can't handle such a species due to >>>>> modifications >>>>> of >>>>> backbone charges when applying N- and C-terminal modifications. To use >>>>> this force field with this system, you need to introduce a new residue >>>>> that >>>>> defines the zwitterion correctly. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> 2015-02-06 13:15 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>: >>>>> >>>>> >>>>>> On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım < >>>>>> ahmedo...@gmail.com> >>>>>> >>>>>> wrote: >>>>>>> >>>>>>> Dear users, >>>>>>> >>>>>>> >>>>>>>> I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, >>>>>>>> with >>>>>>>> the AMBER99SB-ILDN ff. My command: >>>>>>>> pdb2gmx -f protein.pdb -o protein.gro -p protein.top >>>>>>>> >>>>>>>> Fatal error: >>>>>>>> In the chosen force field there is no residue type for 'LYS' as a >>>>>>>> standalone (starting & ending) residue >>>>>>>> >>>>>>>> The pdb2gmx gives this error though terminal residues are prefixed >>>>>>>> with >>>>>>>> N >>>>>>>> and C. >>>>>>>> >>>>>>>> >>>>>>>> Maybe those prefixes are in the wrong columns of your input .pdb >>>>>>>> >>>>>>> file. >>>>>>> >>>>>>> >>>>>>> Could there be something wrong with the input .pdb file? But i >>>>>>> dont >>>>>>> get >>>>>>> >>>>>>> this error with another forcefield, 43a2. >>>>>>>> >>>>>>>> >>>>>>>> GROMOS force fields handle termini differently from AMBER, so >>>>>>>> that's >>>>>>>> >>>>>>> expected. >>>>>>> >>>>>>> Mark >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>>> Ahmet Yıldırım >>>>>>>> -- >>>>>>>> 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. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> >>>>> ================================================== >>>>> >>>>> 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. >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>> ================================================== >>> >>> 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. >>> >>> >> >> >> > -- > ================================================== > > 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. > -- Ahmet Yıldırım -- 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.
