Thanks for your suggestions. Now I am getting the following error during grompp
Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not match (C1 - N) Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not match (C2 - CA) Warning: atom name 6 in topol.top and box_prot_oct_sol.gro does not match (H4 - HA) Warning: atom name 7 in topol.top and box_prot_oct_sol.gro does not match (H5 - CB) Warning: atom name 8 in topol.top and box_prot_oct_sol.gro does not match (C3 - HB1) Warning: atom name 9 in topol.top and box_prot_oct_sol.gro does not match (H6 - HB2) Warning: atom name 10 in topol.top and box_prot_oct_sol.gro does not match (H7 - OG) Warning: atom name 11 in topol.top and box_prot_oct_sol.gro does not match (C4 - HG) Warning: atom name 12 in topol.top and box_prot_oct_sol.gro does not match (H8 - C) Warning: atom name 13 in topol.top and box_prot_oct_sol.gro does not match (H9 - O) Warning: atom name 14 in topol.top and box_prot_oct_sol.gro does not match (C5 - N) Warning: atom name 15 in topol.top and box_prot_oct_sol.gro does not match (H10 - H) Warning: atom name 16 in topol.top and box_prot_oct_sol.gro does not match (H11 - CA) Warning: atom name 17 in topol.top and box_prot_oct_sol.gro does not match (C6 - HA) Warning: atom name 18 in topol.top and box_prot_oct_sol.gro does not match (H12 - CB) Warning: atom name 19 in topol.top and box_prot_oct_sol.gro does not match (H13 - HB1) Warning: atom name 20 in topol.top and box_prot_oct_sol.gro does not match (C7 - HB2) Warning: atom name 21 in topol.top and box_prot_oct_sol.gro does not match (H14 - CG) Warning: atom name 22 in topol.top and box_prot_oct_sol.gro does not match (H15 - HG) Warning: atom name 23 in topol.top and box_prot_oct_sol.gro does not match (C8 - CD1) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 55]: 28782 non-matching atom names atom names from topol.top will be used atom names from box_prot_oct_sol.gro will be ignored The order of atoms in coordinate file and order of [molecules] directive are same. I have checked on the gromacs forum and also the documentation but not able to rectify the problem. This is how I included the octane topology in .top file ######################################### ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" #include "oct.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Ion_chain_A2.itp" ; 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 SOL 565 1-octanol 1 SOL 8422 #################################### Please provide suggestions. On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bipin singh wrote: >> >> Thanks for your inputs. >> I have followed your suggestion and included the .itp for the octane >> molecule (containing atomtype definition for new atoms) in the >> topology file(.top) of the whole system (prot+oct+water). but during >> grompp it produce error and results in termination due to non matching >> numbers (27 atoms of octane molecule) between coordinate file and >> topology file. >> >> >> >> WARNING 1 [file 111-87-5.top, line 15]: >> Overriding atomtype h1 >> >> >> WARNING 2 [file 111-87-5.top, line 17]: >> Overriding atomtype c3 >> >> >> WARNING 3 [file 111-87-5.top, line 19]: >> Overriding atomtype ho >> > > It appears that you have somehow duplicated atom types and they are > overriding each other. > > >> Generated 4656 of the 4656 non-bonded parameter combinations >> Generating 1-4 interactions: fudge = 0.5 >> Generated 4656 of the 4656 1-4 parameter combinations >> Excluding 3 bonded neighbours molecule type '1-octanol' >> Excluding 3 bonded neighbours molecule type 'Protein_chain_A' >> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' >> Excluding 3 bonded neighbours molecule type '1-octanol' >> Excluding 2 bonded neighbours molecule type 'SOL' >> Excluding 2 bonded neighbours molecule type 'SOL' >> >> NOTE 1 [file topol.top, line 55]: >> System has non-zero total charge: -9.999989e-01 >> >> Program grompp, VERSION 4.5.3 >> Source code file: grompp.c, line: 523 >> >> Fatal error: >> number of coordinates in coordinate file (box_oct_sol.gro, 54297) >> does not match topology (topol.top, 54324) >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> > > Did you follow the link? Surely you would have found: > > http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology > > -Justin > > >> ######################################################################3 >> this is how I included the itp for the octane molecule in .top file >> >> ; Include forcefield parameters >> #include "amber99sb-ildn.ff/forcefield.itp" >> #include "octane.itp" >> >> ; Include chain topologies >> #include "topol_Protein_chain_A.itp" >> #include "topol_Ion_chain_A2.itp" >> >> ; 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 565 >> SOL 8495 >> ######################################################################### >> >> ------------------------------------------------------- >> >> Please provide your comments. >> >> On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> bipin singh wrote: >>>> >>>> Thanks for your reply. >>>> >>>> Yes, you are right that these topologies are self supporting and there >>>> is no need to to call any other information. I followed your >>>> suggestions and able to generate a biphasic system of water/octane >>>> containing a protein molecule. But, when I tried grompp on this >>>> biphasic system (containing octane+water+protein), it results in error >>>> even if I include the topologies in forcefield.itp file. >>>> >>>> The error was >>>> >>>> Fatal error: >>>> Atomtype hc not found >>>> For more information and tips for troubleshooting, please check the >>>> GROMACS >>>> website at http://www.gromacs.org/Documentation/Errors >>>> >>> If you introduce a new atomtype in your topology somewhere (presumably in >>> one of the GAFF topologies), then you have to declare them in an >>> [atomtypes] >>> directive in the appropriate place in the .top file. These types are >>> case >>> sensitive as well. For dealing with GAFF-type topologies, assuming you >>> can >>> #include them within whatever AMBER force field you've chosen (up to you >>> to >>> prove), you can do something like: >>> >>> #include "amberXX.ff/forcefield.itp" >>> >>> #include "ligand.itp" >>> >>> [ moleculetype ] >>> ;name nrexcl >>> Protein 3 >>> >>> (etc) >>> >>> The inclusion of the ligand topology (at this specific location) will add >>> the new [atomtypes] at the appropriate level of precedence, before any >>> [moleculetypes] are declared. >>> >>> >>> -Justin >>> >>>> On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul <jalem...@vt.edu> wrote: >>>>> >>>>> >>>>> bipin singh wrote: >>>>>> >>>>>> Thanks for your reply. >>>>>> But as far as I understood, in order to use these GAFF topology (for >>>>>> e.g. to perform simulation using these topologies) with Gromacs we >>>>>> have to incorporate the information from these topologies to the >>>>>> existing Amber forcefields in Gromacs or Is there anyway (Possibility >>>>>> of using Standalone GAFF parameters in Gromacs) to do it without >>>>>> performing this task. >>>>>> >>>>> As David said, the topologies stand on their own. You do not need to >>>>> call >>>>> any further information from anywhere. The .top that you downloaded >>>>> begins >>>>> with a [defaults] directive, declares atom types, and proceeds through >>>>> the >>>>> rest of the topology with explicit parameters. >>>>> >>>>> >>>>>> As you said these topologies are self supporting and we do not need to >>>>>> change ffbonded.itp, but during grompp I got the following error, may >>>>>> be because I have not added the dihedral information. >>>>>> >>>>>> ERROR [file oct.top]: >>>>>> No default Proper Dih. types >>>>>> >>>>>> Please provide your suggestions. >>>>>> >>>>> I certainly don't see how this could have happened. All the dihedral >>>>> parameters are listed explicitly. The fatal error should have printed >>>>> a >>>>> line number in the .top that is problematic, so start by investigating >>>>> there. If you have modified the topology in any way, then undo the >>>>> changes >>>>> and try again. >>>>> >>>>> I did not have any trouble using this .top in an unmodified form, so I >>>>> suspect you've altered it in some way that has broken it. >>>>> >>>>> -Justin >>>>> >>>>> >>>>>> On Mon, Mar 26, 2012 at 17:29, David van der Spoel >>>>>> <sp...@xray.bmc.uu.se> >>>>>> wrote: >>>>>>> >>>>>>> On 2012-03-26 13:55, bipin singh wrote: >>>>>>>> >>>>>>>> Hello all, >>>>>>>> >>>>>>>> I am using the GAFF topology provided for octan-1-ol at Gromacs >>>>>>>> liquid >>>>>>>> database (http://virtualchemistry.org/molecules/111-87-5/index.php). >>>>>>>> I >>>>>>>> have incorporated all the parameters >>>>>>>> for atoms, bonds and non-bonded interaction type in the forcefield >>>>>>>> (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but >>>>>>>> I >>>>>>>> am not sure how to add the dihedraltypes information in ffbonded.itp >>>>>>>> from the GAFF topology as to add this information I need the phase >>>>>>>> and >>>>>>>> kd for each dihedral. Is this information is available in the GAFF >>>>>>>> topology provided in the Gromacs database ? >>>>>>>> >>>>>>>> >>>>>>> This topology is self supporting and you do not need anything else in >>>>>>> ffbonded.itp. >>>>>>> >>>>>>> You should be careful merging such parameters with an existing force >>>>>>> field, >>>>>>> because strictly speaking these are different force fields. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> David van der Spoel, Ph.D., Professor of Biology >>>>>>> Dept. of Cell & Molec. Biol., Uppsala University. >>>>>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>>>>>> sp...@xray.bmc.uu.se http://folding.bmc.uu.se >>>>>>> -- >>>>>>> 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 >> >> >> >> > > -- > ======================================== > > 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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