Hi Justin, There is no errors in dihedral but I got 4 warnings in ffbonded.itp. Is there any suggestions from you.
WARNING 1 [file ffbonded.itp, line 2817]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 180 5.86 1 180 5.86 1 new: LNL LH2 LC2 LOS 1 0.00 8.62 3 WARNING 2 [file ffbonded.itp, line 2820]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LC2 LOS LP LOS 1 0.00 3.19 3 WARNING 3 [file ffbonded.itp, line 2821]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 3.19 3 0 3.19 3 new: LOS LP LOS LC2 1 0.00 5.09 2 WARNING 4 [file ffbonded.itp, line 2822]: Overriding Proper Dih. parameters. Use dihedraltype 4 to allow several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LOS LP LOS LC2 1 0.00 3.19 3 Thanks --Rama On Tue, Sep 10, 2013 at 12:34 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote: > >> Adding parameters can be a little bit of a pain, you could instead change >> the atom types in the molecule parameter, to ones that have defined angles >> and bond types with each other. Of course, you would need to make sure >> that >> you dont assign sp2 with sp3 atoms, or aromatic with non aromatic etc. >> Check out ffbonded in the appropriate forcefield folder to see which >> atomtypes have defined bond types. Check out atomtypes.atp to see all the >> atom types for the forcefield >> >> > Given that at present the issue involves only protein and lipids, the > approach of swapping around atom types is very dangerous, probably more so > than assigning bonded parameters by analogy. I don't recall the OP ever > telling us what the force field is, though, so it's hard to know all of > what we're dealing with here. > > > -Justin > > >> On Tue, Sep 10, 2013 at 6:40 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 9/10/13 9:33 AM, Rama Krishna Koppisetti wrote: >>> >>> Hi Justin, >>>> >>>> It is which part in the force field. Exactly which file I have to look >>>> to >>>> overcome this errors. >>>> >>>> >>>> Go to the line number in the .top indicated in the error message and >>> determine the atom types. This will tell you the sequence of atom types >>> involved in the R-B dihedral that is missing. In theory, you would then >>> add missing parameters to ffbonded.itp, if they exist. >>> >>> -Justin >>> >>> >>> On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul <jalem...@vt.edu> >>> wrote: >>> >>>> >>>> >>>> >>>>> On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: >>>>> >>>>> Hi Justin, >>>>> >>>>>> >>>>>> This is another type of error while running energy minimization: >>>>>> what to do for these type of errors. >>>>>> >>>>>> >>>>>> They're exactly the same as the dihedral error from before. You're >>>>>> >>>>> using >>>>> parameters that don't exist in the force field. >>>>> >>>>> -Justin >>>>> >>>>> ERROR 218 [file topol.top, line 23487]: >>>>> >>>>> No default Ryckaert-Bell. types >>>>>> >>>>>> >>>>>> ERROR 219 [file topol.top, line 23499]: >>>>>> No default Ryckaert-Bell. types >>>>>> >>>>>> >>>>>> ERROR 220 [file topol.top, line 23500]: >>>>>> No default Ryckaert-Bell. types >>>>>> >>>>>> >>>>>> ERROR 221 [file topol.top, line 23501]: >>>>>> No default Ryckaert-Bell. types >>>>>> >>>>>> >>>>>> ERROR 222 [file topol.top, line 23502]: >>>>>> No default Ryckaert-Bell. types >>>>>> >>>>>> >>>>>> ERROR 223 [file topol.top, line 23503]: >>>>>> No default Ryckaert-Bell. types >>>>>> >>>>>> >>>>>> ERROR 224 [file topol.top, line 23515]: >>>>>> No default Ryckaert-Bell. types >>>>>> >>>>>> >>>>>> --Rama >>>>>> >>>>>> >>>>>> On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul <jalem...@vt.edu> >>>>>> wrote: >>>>>> >>>>>> >>>>>> >>>>>> On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: >>>>>>> >>>>>>> Hi Justin, >>>>>>> >>>>>>> >>>>>>>> I included 1 DMPC molecule parameters in the file should I need to >>>>>>>> include >>>>>>>> 128 molecules parameters in the file .rtp. >>>>>>>> >>>>>>>> >>>>>>>> No. Residue definitions are used any time they are encountered >>>>>>>> in >>>>>>>> the >>>>>>>> >>>>>>>> coordinate file. There is no need for such redundancy at the force >>>>>>> field >>>>>>> level. >>>>>>> >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>> -- >>>>>>> ==============================********==================== >>>>>>> >>>>>>> >>>>>>> Justin A. Lemkul, Ph.D. >>>>>>> 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 >>>>>>> >>>>>>> jalemkul@outerbanks.umaryland.********edu <jalemkul@outerbanks.** >>>>>>> umaryland.edu >>>>>>> <jalemkul@outerbanks.**umaryla**nd.edu<http://umaryland.edu> >>>>>>> <jalemkul@outerbanks.**umaryland.edu<jalem...@outerbanks.umaryland.edu> >>>>>>> >>> >>>>>>> | (410) >>>>>>> 706-7441 >>>>>>> >>>>>>> ==============================********==================== >>>>>>> -- >>>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>>> http://lists.gromacs.org/********mailman/listinfo/gmx-users<http://lists.gromacs.org/******mailman/listinfo/gmx-users> >>>>>>> <ht**tp://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> >>>>>>> > >>>>>>> <htt**p://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> >>>>>>> <h**ttp://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>>>> > >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> <htt**p://lists.gromacs.org/****mailman/**listinfo/gmx-users<http://lists.gromacs.org/**mailman/**listinfo/gmx-users> >>>>>>> <h**ttp://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>>>> > >>>>>>> <h**ttp://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>>>> > >>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>>> * Please search the archive at http://www.gromacs.org/** >>>>>>>> >>>>>>> Support/Mailing_Lists/Search<****h**ttp://www.gromacs.org/**** >>>>>>> Support/** <http://www.gromacs.org/**Support/**><http://www.gromacs. >>>>>>> **org/Support/** <http://www.gromacs.org/Support/**>> >>>>>>> Mailing_Lists/Search<http://****www.gromacs.org/Support/**<http://www.gromacs.org/Support/**> >>>>>>> Mailing_Lists/Search<http://**www.gromacs.org/Support/** >>>>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search> >>>>>>> > >>>>>>> >>>>>>>> before >>>>>>>>> >>>>>>>> posting! >>>>>>> >>>>>>> * Please don't post (un)subscribe requests to the list. 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Read http://www.gromacs.org/******** >>>>>>> Support/Mailing_Lists<http://www.gromacs.org/******Support/Mailing_Lists> >>>>>>> <http://**www.gromacs.org/****Support/**Mailing_Lists<http://www.gromacs.org/****Support/Mailing_Lists> >>>>>>> > >>>>>>> <http://**www.gromacs.org/****Support/**Mailing_Lists<http://www.gromacs.org/**Support/**Mailing_Lists> >>>>>>> <http:/**/www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>>>>> > >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> <http://**www.gromacs.org/****Support/**Mailing_Lists<http://www.gromacs.org/**Support/**Mailing_Lists> >>>>>>> <http:/**/www.gromacs.org/Support/****Mailing_Lists<http://www.gromacs.org/Support/**Mailing_Lists> >>>>>>> > >>>>>>> <http:/**/www.gromacs.org/**Support/**Mailing_Lists<http://www.gromacs.org/Support/**Mailing_Lists> >>>>>>> <http:/**/www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>>>> > >>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> >>>>>> ==============================******==================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> 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 >>>>> >>>>> jalemkul@outerbanks.umaryland.******edu <jalemkul@outerbanks.** >>>>> umaryland.edu >>>>> <jalemkul@outerbanks.**umaryland.edu<jalem...@outerbanks.umaryland.edu>>> >>>>> | (410) >>>>> 706-7441 >>>>> >>>>> ==============================******==================== >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/******mailman/listinfo/gmx-users<http://lists.gromacs.org/****mailman/listinfo/gmx-users> >>>>> <htt**p://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>> > >>>>> <htt**p://lists.gromacs.org/**mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/**listinfo/gmx-users> >>>>> <h**ttp://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> > >>>>> >>>>>> >>>>>> * Please search the archive at http://www.gromacs.org/** >>>>> Support/Mailing_Lists/Search<**h**ttp://www.gromacs.org/**Support/**<http://www.gromacs.org/Support/**> >>>>> Mailing_Lists/Search<http://**www.gromacs.org/Support/** >>>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search> >>>>> >>before >>>>> posting! >>>>> * Please don't post (un)subscribe requests to the list. 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Lemkul, Ph.D. >>> 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 >>> >>> jalemkul@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>> umaryland.edu <jalem...@outerbanks.umaryland.edu>> | (410) >>> 706-7441 >>> >>> ==============================****==================== >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> * Please don't post (un)subscribe requests to the list. 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Lemkul, Ph.D. > 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 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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? 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