Dear Dr. Justin, If the bond types have not added, following errors occuring with grompp,
1) ERROR 1 [file topol.top, line 108]: No default Bond types 2) ERROR 2 [file topol.top, line 168]: No default Angle types 3) ERROR 3 [file topol.top, line 426]: No default Ryckaert-Bell. types Atom types are seems to be correct as i derived them from atomtype.atp file. If the interaction don't cover by the force field, how can I define them in ffbonded.itp file ? Regards On Sep 19, 2016 3:57 AM, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 9/18/16 2:26 PM, Sameer Edirisinghe wrote: > >> Dear Dr. Justin, >> >> Now i can understand what what i have mistaken there. How can i derive >> [bondtypes] >> for bonds i have used in .rtp file ? >> >> > Determine if you need to in the first place. If grompp gives you errors > about missing parameters, first verify that your choice of atom types is > correct. Then, if there are in fact interactions that the force field > doesn't cover: > > 1. Make sure your choice of force field was appropriate > 2. Parametrize them in a manner consistent with the parent force field > > -Justin > > Regards >> >> On Sun, Sep 18, 2016 at 11:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 9/18/16 2:06 PM, Sameer Edirisinghe wrote: >>> >>> Dear Dr. Justin, >>>> >>>> If atom names names cant use in ffbonded.itp file how should i add bond >>>> interaction used in .rtp file to ff..itp file ? this is the part i >>>> dont >>>> understand. Do i need to modify ffnonbonded.itp file to correct the >>>> "Unknown >>>> bond_atomtype' error which occurring while runing grompp ? If so how i >>>> should modify ffnonbonded.itp (I have attached my .rtp file herewith) >>>> >>>> >>>> You do not need to modify ffnonbonded.itp. >>> >>> You added an atom name in ffbonded.itp - this makes no sense and you >>> cannot do it. Bonded and nonbonded interactions are defined by type. >>> >>> You must use atom names only in .rtp files, because the .rtp entry tells >>> pdb2gmx which atoms are bonded, and how. You can't do that by type >>> because >>> that is not a unique way to identify connectivity. The list of [bonds] >>> in >>> the .rtp just tells pdb2gmx which atoms are connect, it is separate from >>> a >>> [bondtypes] directive, which says what parameters are assigned to each >>> interaction type. >>> >>> -Justin >>> >>> >>> >>> Regards >>>> Sameera >>>> >>>> On Sun, Sep 18, 2016 at 10:45 PM, Justin Lemkul <jalem...@vt.edu> >>>> wrote: >>>> >>>> >>>> >>>>> On 9/18/16 1:12 PM, Sameer Edirisinghe wrote: >>>>> >>>>> Dear Dr. Justin, >>>>> >>>>>> >>>>>> Thanks for the reply. Following is the whole .rtp file i used. ( As >>>>>> you >>>>>> said it was generated by using PRODRG) >>>>>> >>>>>> >>>>>> You shouldn't use the charges from PRODRG. They assume a united-atom >>>>>> >>>>> force field, and are of very low quality. You can't force them into >>>>> working with OPLS-AA. It's fundamentally wrong. >>>>> >>>>> If you want free help with a problem, you have to provide full >>>>> information. Fragments of .rtp files are not helpful and it's a waste >>>>> of >>>>> time for those who are trying to give you advice. >>>>> >>>>> >>>>> [ bondedtypes ] >>>>> >>>>> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 >>>>>> RemoveDih >>>>>> 1 1 3 1 >>>>>> >>>>>> ; MDI >>>>>> [ MD ] >>>>>> [ atoms ] >>>>>> CAY opls_135 0 1 >>>>>> CAX opls_135 0.048 2 >>>>>> CAW opls_135 0.047 2 >>>>>> CAV opls_135 0.144 2 >>>>>> OAU opls_154 -0.112 2 >>>>>> CAS opls_131 0.219 2 >>>>>> OAT opls_236 -0.41 2 >>>>>> NAO opls_900 0.073 2 >>>>>> HAO opls_250 -0.009 2 >>>>>> CAE opls_260 0.056 3 >>>>>> CAF opls_145 -0.018 3 >>>>>> HAF opls_140 0.004 3 >>>>>> CAA opls_145 -0.018 3 >>>>>> HAA opls_140 0.004 3 >>>>>> CAD opls_145 -0.018 3 >>>>>> HAD opls_140 0.004 3 >>>>>> CAC opls_145 -0.018 3 >>>>>> HAC opls_140 0.004 3 >>>>>> CAB opls_145 -0.022 4 >>>>>> CAG opls_071 0.044 4 >>>>>> CAH opls_145 -0.022 4 >>>>>> CAM opls_145 -0.008 5 >>>>>> HAM opls_140 0.008 5 >>>>>> CAL opls_145 -0.008 6 >>>>>> HAL opls_140 0.008 6 >>>>>> CAI opls_145 -0.008 7 >>>>>> HAI opls_140 0.008 7 >>>>>> CAJ opls_145 -0.008 8 >>>>>> HAJ opls_140 0.008 8 >>>>>> CAK opls_145 0.072 9 >>>>>> NAN opls_900 0.072 9 >>>>>> HAN opls_250 -0.009 9 >>>>>> CAP opls_131 0.214 9 >>>>>> OAQ opls_236 -0.419 9 >>>>>> OAR opls_154 -0.115 9 >>>>>> CAZ opls_135 0.14 9 >>>>>> CBA opls_135 0.045 9 >>>>>> CBB opls_135 0.01 10 >>>>>> CBC opls_135 -0.01 10 >>>>>> HA1 opls_140 -0.013 1 >>>>>> HA2 opls_140 -0.013 1 >>>>>> HA3 opls_140 -0.014 1 >>>>>> HAZ opls_140 -0.013 1 >>>>>> HA0 opls_140 -0.013 1 >>>>>> HAX opls_140 -0.013 1 >>>>>> HAY opls_140 -0.013 1 >>>>>> HAV opls_140 -0.013 1 >>>>>> HAW opls_140 -0.013 1 >>>>>> HAG opls_140 -0.013 1 >>>>>> HAH opls_140 -0.013 1 >>>>>> HA4 opls_140 -0.013 1 >>>>>> HA5 opls_140 -0.013 1 >>>>>> HBA opls_140 -0.013 1 >>>>>> HBB opls_140 -0.013 1 >>>>>> HBC opls_140 -0.013 1 >>>>>> HBD opls_140 -0.013 1 >>>>>> HBF opls_140 -0.013 1 >>>>>> HBG opls_140 -0.013 1 >>>>>> HBE opls_140 -0.013 1 >>>>>> [ bonds ] >>>>>> CAY HA1 >>>>>> CAY HA2 >>>>>> CAY HA3 >>>>>> CAX CAY >>>>>> CAX HAZ >>>>>> CAX HA0 >>>>>> CAX CAW >>>>>> CAW HAX >>>>>> CAW HAY >>>>>> CAW CAV >>>>>> CAV HAV >>>>>> CAV HAW >>>>>> CAV OAU >>>>>> CAS OAU >>>>>> CAS OAT >>>>>> CAS NAO >>>>>> NAO HAO >>>>>> CAE NAO >>>>>> CAE CAF >>>>>> CAE CAD >>>>>> CAF HAF >>>>>> CAF CAA >>>>>> CAA HAA >>>>>> CAB CAA >>>>>> CAD HAD >>>>>> CAD CAC >>>>>> CAC HAC >>>>>> CAB CAC >>>>>> CAB CAG >>>>>> CAG HAG >>>>>> CAG HAH >>>>>> CAH CAG >>>>>> CAH CAM >>>>>> CAH CAI >>>>>> CAM HAM >>>>>> CAM CAL >>>>>> CAL HAL >>>>>> CAK CAL >>>>>> CAI HAI >>>>>> CAI CAJ >>>>>> CAJ HAJ >>>>>> CAK CAJ >>>>>> CAK NAN >>>>>> NAN HAN >>>>>> CAP NAN >>>>>> CAP OAQ >>>>>> CAP OAR >>>>>> CAZ OAR >>>>>> CAZ HA4 >>>>>> CAZ HA5 >>>>>> CAZ CBA >>>>>> CBA HBA >>>>>> CBA HBB >>>>>> CBA CBB >>>>>> CBB HBC >>>>>> CBB HBD >>>>>> CBB CBC >>>>>> CBC HBF >>>>>> CBC HBG >>>>>> CBC HBE >>>>>> >>>>>> ffbonded.itp file modified with the relevant bonds as below (part has >>>>>> mentioned below) >>>>>> >>>>>> CAY HA1 1 0.10900 284512.0 ; >>>>>> CAY HA2 1 0.10900 284512.0 ; >>>>>> CAY HA3 1 0.10900 284512.0 ; >>>>>> CAX CAY 1 0.15220 265265.6 ; >>>>>> CAX HAZ 1 0.10900 284512.0 ; >>>>>> >>>>>> >>>>>> >>>>>> As I said before, you cannot use atom names in ffbonded.itp. >>>>>> >>>>> >>>>> I know atom name is irrelevant but im bit confused how to write .rtp >>>>> >>>>> without names for my 59 atom molecule. >>>>>> >>>>>> >>>>>> The .rtp file *does* use atom names. See the manual. That part is >>>>>> >>>>> fine. >>>>> What you cannot do is try to assign parameters using names. Those >>>>> require >>>>> types. >>>>> >>>>> -Justin >>>>> >>>>> >>>>> >>>>> regards >>>>> >>>>>> >>>>>> On Sun, Sep 18, 2016 at 10:09 PM, Justin Lemkul <jalem...@vt.edu> >>>>>> wrote: >>>>>> >>>>>> >>>>>> >>>>>> On 9/18/16 12:30 PM, Sameer Edirisinghe wrote: >>>>>>> >>>>>>> Dear users, >>>>>>> >>>>>>> There is one thing i cannot clarify from gromacs manual which is >>>>>>>> about >>>>>>>> following error occurred while running grompp >>>>>>>> >>>>>>>> Fatal error: >>>>>>>> Unknown bond_atomtype CAY >>>>>>>> >>>>>>>> I used to create .rtp file from atom types which are already >>>>>>>> defined >>>>>>>> in >>>>>>>> atomtype.atp file. But still above error occurring while running >>>>>>>> grompp. >>>>>>>> Not sure should i add again thes atoms to atp file and if so how to >>>>>>>> add >>>>>>>> them. Part of my rtp file is as below, I have modified the >>>>>>>> ffbonded.itp >>>>>>>> (only bond types added) successfully. >>>>>>>> >>>>>>>> >>>>>>>> What did you add to ffbonded.itp? Whatever it was is causing an >>>>>>>> error. >>>>>>>> >>>>>>>> Based on the .rtp entry below, it looks like you tried to use atom >>>>>>> names >>>>>>> in >>>>>>> ffbonded.itp. That's not right. All interactions (bonded and >>>>>>> nonbonded) >>>>>>> are defined by atom type. The name is irrelevant. If you're >>>>>>> re-using >>>>>>> only >>>>>>> OPLS-AA atom types, most of the bonded interactions should be present >>>>>>> already. >>>>>>> >>>>>>> [ bondedtypes ] >>>>>>> >>>>>>> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 >>>>>>> >>>>>>>> RemoveDih >>>>>>>> 1 1 3 1 >>>>>>>> >>>>>>>> >>>>>>>> You're missing entries here if you're trying to create an >>>>>>>> OPLS-derived >>>>>>>> >>>>>>>> force field. Look at oplsaa.ff/aminoacids.rtp >>>>>>> >>>>>>> ; MDI >>>>>>> >>>>>>> [ MD ] >>>>>>> >>>>>>>> [ atoms ] >>>>>>>> CAY opls_135 0.000 1 >>>>>>>> CAX opls_135 0.048 2 >>>>>>>> CAW opls_135 0.047 2 >>>>>>>> CAV opls_135 0.144 2 >>>>>>>> OAU opls_154 -0.112 2 >>>>>>>> >>>>>>>> >>>>>>>> This can't possibly be right. You've defined only heavy atoms >>>>>>>> (OPLS-AA >>>>>>>> >>>>>>>> is >>>>>>> an all-atom force field, so there should be H) and the net charge of >>>>>>> this >>>>>>> residue is +0.117, which is physical nonsense. Based on the names >>>>>>> and >>>>>>> suspect charges, it looks like you're just porting over a PRODRG >>>>>>> united-atom topology and trying to call it OPLS-AA. That's not going >>>>>>> to >>>>>>> work. >>>>>>> >>>>>>> Note that you also need [bonds] if you want the residue to actually >>>>>>> be >>>>>>> chemically reasonable, otherwise it's just a collection of atoms >>>>>>> sitting >>>>>>> near one another, which will immediately explode if you try to run a >>>>>>> simulation. >>>>>>> >>>>>>> -Justin >>>>>>> >>>>>>> -- >>>>>>> ================================================== >>>>>>> >>>>>>> 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. >>> >>> > -- > ================================================== > > 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? 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