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 ?
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. > -- 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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