A lot of thanks to your "charitable mood" now the things has been resolved :) . Thanks again.
On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bipin singh wrote: >> >> Thanks again >> > > For the record, I didn't ask that you send me your files so I could > troubleshoot for you. Luckily for you I'm in a charitable mood this > morning, so I took a look ;) > > Your problem is that you have a [molecules] directive in oct.itp. Please > refer to the documentation for the difference between a .top topology and a > .itp topology: > > http://www.gromacs.org/Documentation/File_Formats/.itp_File > > The presence of this [molecules] directive tells grompp that the first thing > it should expect is a block of octanol, when in fact your coordinate file > has the protein first (starting with Ser-Leu, as I suspected). You then > have "1-octanol 1" in your topol.top, which says you're including another > random octanol molecule somewhere later. > > You need a single [molecules] directive in the .top, which must match the > order of the coordinate file. Once you've got that, things should work > fine. > > -Justin > > >>> From the error It seems that I have placed the octane molecule before >> >> the protein but it is not the case, I dont know why grompp is reading >> parameters for octane first and expecting it to match with protein. I >> know that its my problem and I have to think about >> that but just for the reference for you I am attaching the coordinate >> and topology files. >> >> On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> bipin singh wrote: >>>> >>>> Thanks for your inputs. >>>> >>>> I have checked the coordinate file thoroughly and the order of atoms >>>> are same as defined in the [molecules] directive. >>>> I really do not able to find out the source of the error. >>>> >>> Looking closer at the error, what's happening is your octanol molecule is >>> in >>> a place where the topology expects the amino acid sequence Ser-Leu. >>> Perhaps >>> that will help you track down the source of the problem. It seems to me >>> that your octanol molecule occurs earlier in the coordinate file than it >>> does in the topology. >>> >>> If you still can't locate the problem, then you can always start over >>> building your system in a known order, checking the alignment of the >>> coordinate file and topology at every step. >>> >>> -Justin >>> >>> >>>> On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul <jalem...@vt.edu> wrote: >>>>> >>>>> >>>>> Biswajit Gorai wrote: >>>>>> >>>>>> Dear Bipin, >>>>>> Edit your topology file as: >>>>>> >>>>>> ########################################### >>>>>> ; Include forcefield parameters >>>>>> #include "amber99sb-ildn.ff/forcefield.itp" >>>>>> >>>>>> ; Include chain topologies >>>>>> #include "topol_Protein_chain_A.itp" >>>>>> #include "topol_Ion_chain_A2.itp" >>>>>> >>>>>> *#include "oct.itp"* >>>>>> >>>>> If oct.itp introduces new atom types (as the original .top does, for >>>>> GAFF), >>>>> placing this topology here will result in a fatal error since there is >>>>> a >>>>> new >>>>> [atomtypes] directive that is introduced after the protein >>>>> [moleculetype]. >>>>> If oct.itp does not introduce any new atom types, its location within >>>>> the >>>>> system topology is irrelevant. >>>>> >>>>>> ; Include water topology >>>>>> #include "amber99sb-ildn.ff/tip3p.itp" >>>>>> >>>>>> #ifdef POSRES_WATER >>>>>> ; Position restraint for each water oxygen >>>>>> [ position_restraints ] >>>>>> ; i funct fcx fcy fcz >>>>>> 1 1 1000 1000 1000 >>>>>> #endif >>>>>> >>>>>> ; Include topology for ions >>>>>> #include "amber99sb-ildn.ff/ions.itp" >>>>>> >>>>>> [ system ] >>>>>> ; Name >>>>>> Protein in water >>>>>> >>>>>> [ molecules ] >>>>>> ; Compound #mols >>>>>> Protein_chain_A 1 >>>>>> Ion_chain_A2 1 >>>>>> *1-octanol 1 >>>>>> * >>>>>> *SOL 8987* >>>>> >>>>> >>>>> Depending on the order of the coordinate file, it may not be possible >>>>> to >>>>> merge the SOL entries in this way. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> -- >>>>> ======================================== >>>>> >>>>> Justin A. Lemkul >>>>> Ph.D. Candidate >>>>> ICTAS Doctoral Scholar >>>>> MILES-IGERT Trainee >>>>> Department of Biochemistry >>>>> Virginia Tech >>>>> Blacksburg, VA >>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>>> >>>>> ======================================== >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>>> Please don't post (un)subscribe requests to the list. Use the www >>>>> interface >>>>> or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ----------------------- Regards, Bipin Singh -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. 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