Thank you very much... But I am not going to use any parent molecules like protein or DNA. I would like to perform the gromacs simulation for this unknown molecule. First few lines of my topology file..
"; ; File 'topol.top' was generated ; By user: kollan (506) ; On host: master.localdomain ; At date: Sun Nov 2 20:28:10 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.3 ; ; Command line was: ; pdb2gmx -f A-T.pdb -o A-T1.pdb -p topol.top ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters # include "A-T.itp" ; ---- ; Built itp for A-T.mol2 ; by user vzoete Mon Oct 27 06:32:46 CET 2014 ; ---- ; [ atomtypes ] " The yellow colored lines are first seven line A-T.itp file And the error was ""Fatal error: Syntax error - File A-T.itp, line 7 Last line read: '[ atomtypes ]' Invalid order for directive atomtypes" Please help me.. On Mon, Nov 3, 2014 at 1:28 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/2/14 11:32 AM, Kalyanashis Jana wrote: > >> Thank you so much... I have tried to run the grompp step according to you. >> But it is showing >> "Fatal error: >> Syntax error - File A-T.itp, line 7 >> Last line read: >> '[ atomtypes ]' >> Invalid order for directive atomtypes" >> I have attached the .itp file and .top file. >> Please kindly tell me, what to do now.. >> >> > Force-field level directives must be declared before molecule-level > directives. So if your ligand requires new bonded or nonbonded parameters, > or new atom types, it must be #included before the declaration of any > [moleculetype]. So put your #include statement for the ligand topology > immediately after the #include statement for the parent force field. > > -Justin > > > On Sun, Nov 2, 2014 at 9:15 PM, Victor Rosas Garcia < >> rosas.vic...@gmail.com> >> wrote: >> >> just put the itp file in your working directory, and include it in the >>> top file of your system, so that Gromacs can find it. >>> >>> Hope this helps. >>> >>> Victor >>> >>> 2014-11-02 8:54 GMT-06:00 Kalyanashis Jana <kalyan.chem...@gmail.com>: >>> >>>> Dear all, >>>> I am trying to run a gromacs simulation using an .itp file of an unknown >>>> molecule ( non protein and DNA). I don't want to put the .itp file in a >>>> forcefield folder and I would like put it in my working directory. Can >>>> >>> you >>> >>>> please tell me, what is procedure to finish the energy minimization? >>>> >>> Please >>> >>>> help me.. >>>> Thanks in advance, >>>> Kalyanashis >>>> >>>> -- >>>> Kalyanashis Jana >>>> email: kalyan.chem...@gmail.com >>>> -- >>>> 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. > -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- 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.