Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Thanks Justin. I will then add manually the constraints on the topology file. Paolo Il giorno gio 7 mag 2020 alle ore 14:56 Justin Lemkul ha scritto: > > > On 5/7/20 8:53 AM, Paolo Costa wrote: > > Dear Justin > > > > that means when I generate the topology file by pdb2gmx I will add > manually > > the section [constraints] on it? > > I suggest you look into the manual to understand different ways of > applying constraints. You can either convert bonds into constraints via > the "constraints" .mdp option, in which case the force constants are > irrelevant but the equilibrium lengths matter, or you do not define any > bonds and manually write in the [constraints]. It depends on how you > need to treat the system. I know nothing about POMs so I can't comment > specifically. If the species is treated as a fully rigid entity (not > something GROMACS is really well suited for), then you should probably > be writing the topology manually because you will have lots of bonds to > non-sequential atoms. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Dear Justin that means when I generate the topology file by pdb2gmx I will add manually the section [constraints] on it? Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:50 Justin Lemkul ha scritto: > > > On 5/7/20 8:47 AM, Paolo Costa wrote: > > Dear Justin, > > > > I thought too. > > In case, could you please indicate me how I can constrain the interatomic > > distance of a desired molecule, in such case the POM molecule? > > Define [constraints] in the topology for all relevant interatomic > distances. > > -Justin > > > Thanks a lot. > > > > Paolo > > > > Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul > ha > > scritto: > > > >> > >> On 5/7/20 8:41 AM, Paolo Costa wrote: > >>> Dear Justin, > >>> > >>> thanks a lot for your valuable information. > >>> The system (Keggin anion, POM) I am trying to simulate is almost > >> identical > >>> to the one already studied in literature (doi: 10.1021/jp077098p). > >>> In the SI of this work, the authors stated "*Keggin anions are treated > as > >>> rigid particles thus keeping constant the distances between the > different > >>> metal and oxygen atom".* > >>> That means they did not parametrize the bonded interactions for such > >>> molecule, isn't? > >> That sounds to me like all interatomic distances were fixed via > >> constraints, but you should contact the corresponding author to be sure, > >> and ask for example inputs. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> == > >> > >> -- > >> 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. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Dear Justin, I thought too. In case, could you please indicate me how I can constrain the interatomic distance of a desired molecule, in such case the POM molecule? Thanks a lot. Paolo Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul ha scritto: > > > On 5/7/20 8:41 AM, Paolo Costa wrote: > > Dear Justin, > > > > thanks a lot for your valuable information. > > The system (Keggin anion, POM) I am trying to simulate is almost > identical > > to the one already studied in literature (doi: 10.1021/jp077098p). > > In the SI of this work, the authors stated "*Keggin anions are treated as > > rigid particles thus keeping constant the distances between the different > > metal and oxygen atom".* > > That means they did not parametrize the bonded interactions for such > > molecule, isn't? > > That sounds to me like all interatomic distances were fixed via > constraints, but you should contact the corresponding author to be sure, > and ask for example inputs. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Info regarding restrained minimization, equilibration & production
Dear Justin, thanks a lot for your valuable information. The system (Keggin anion, POM) I am trying to simulate is almost identical to the one already studied in literature (doi: 10.1021/jp077098p). In the SI of this work, the authors stated "*Keggin anions are treated as rigid particles thus keeping constant the distances between the different metal and oxygen atom".* That means they did not parametrize the bonded interactions for such molecule, isn't? Thanks. Paolo Il giorno gio 7 mag 2020 alle ore 14:20 Justin Lemkul ha scritto: > > > On 5/6/20 11:35 AM, Paolo Costa wrote: > > Dear Gromacs users, > > > > I am interested on studying the interaction between large metal cluster > > anions (polyoxometallates, POM) with different organic cations (e.g > > perylenes, etc..) in water. > > I have already the non bonded parameters of POMs from literature, while > the > > bonded parameters I calculated from Gaussian and VFFDT software. > > If I do not apply a position restraining force on the POM atoms, the POM > > structure gets distorted too much from the experimental one. I guess this > > is due to the lack of a good force field parametrization for > > metal-containing compound. > > *Thus, my question is the following:* > > *can I keep applying a position restraining force on POM atoms during the > > minimization, equilibration and production steps or is it conceptually > > wrong?* > > If you're restraining a configuration because the force field is so bad, > I'd immediately be skeptical of the quality of any simulation. Bonded > parameters are generally easy to reproduce and probably aren't the > source of your problem if you've implemented them carefully, but if > you're trying to combine new bonded parameters with existing nonbonded > parameters, you need to do careful validation on a known system. > > If your system doesn't work, you should back up and make sure you can > reproduce a published study using the same parameters and not ones of > your creation. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
[gmx-users] Info regarding restrained minimization, equilibration & production
Dear Gromacs users, I am interested on studying the interaction between large metal cluster anions (polyoxometallates, POM) with different organic cations (e.g perylenes, etc..) in water. I have already the non bonded parameters of POMs from literature, while the bonded parameters I calculated from Gaussian and VFFDT software. If I do not apply a position restraining force on the POM atoms, the POM structure gets distorted too much from the experimental one. I guess this is due to the lack of a good force field parametrization for metal-containing compound. *Thus, my question is the following:* *can I keep applying a position restraining force on POM atoms during the minimization, equilibration and production steps or is it conceptually wrong?* Thanks. Best regards, Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Error No default Proper Dih. types
Dear Justin, thanks a lot. Paolo Il giorno dom 26 apr 2020 alle ore 22:33 Justin Lemkul ha scritto: > > > On 4/26/20 3:53 PM, Paolo Costa wrote: > > Dear Justin, > > > > thanks for your extra description. Very nice! > > Last doubt, which values of "phase" and "pn" should I use for [ > > dihedraltypes ]? > > If the force constant is zero, the remaining parameters are irrelevant. > > -Justin > > > Thanks again. > > > > Paolo > > > > Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul > ha > > scritto: > > > >> > >> On 4/26/20 2:08 PM, Paolo Costa wrote: > >>> Dear Justin, > >>> > >>> thanks a lot for your quick reply and useful information. > >>> Thus, I will go through to all the dihedral terms and define zero the > >>> corresponding force constant as you suggested. In any case, I guess it > >> will > >>> be too much work to calculate also the force constant for the torsion > >> angle > >>> rotation. > >> Metals are usually the bridge point between multiple groups and as such > >> their dihedrals are all coupled and not generally considered "soft" > >> (rotatable). So the conformational energetics of these molecules usually > >> involves only bonds and angles in terms of internal parameters. > >> > >> -Justin > >> > >>> Thanks again. > >>> > >>> Paolo > >>> > >>> Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul < > jalem...@vt.edu> > >> ha > >>> scritto: > >>> > >>>> On 4/26/20 1:57 PM, Paolo Costa wrote: > >>>>> Dear Gromacs users, > >>>>> > >>>>> within Amber99 force field I created a new molecule, > polyoxometallate, > >> by > >>>>> creating a new .rtp file and modifying the atomtypes.atp, > >> ffnonbonded.itp > >>>>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ > parameters > >>>>> from known works, while the parameters for the bonding interactions I > >>>>> determined by Gaussian together with VFFDT software. > >>>>> I did not insert any parameters for the dihedral angles since the > >> VFFTDT > >>>>> software does not calculated them. However as written in the related > >>>> paper > >>>>> (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation > >>>> related > >>>>> to metals can often be ignored".* > >>>>> Does somebody knows how to overcome such error in Gromacs? > >>>> pdb2gmx generates all possible angles and dihedrals, as determined by > >>>> the bonds that are defined in the .rtp entry. Thus, you likely have > >>>> dihedrals in the topology in which one of the participating atoms is > the > >>>> metal. You have to have parameters for all defined interactions, but > it > >>>> is true that dihedral terms are not typically used in this case. The > >>>> simplest solution is to define dihedrals with zero force constants so > >>>> they do not contribute to the forces in the system. > >>>> > >>>> -Justin > >>>> > >>>> -- > >>>> == > >>>> > >>>> Justin A. Lemkul, Ph.D. > >>>> Assistant Professor > >>>> Office: 301 Fralin Hall > >>>> Lab: 303 Engel Hall > >>>> > >>>> Virginia Tech Department of Biochemistry > >>>> 340 West Campus Dr. > >>>> Blacksburg, VA 24061 > >>>> > >>>> jalem...@vt.edu | (540) 231-3129 > >>>> http://www.thelemkullab.com > >>>> > >>>> == > >>>> > >>>> -- > >>>> 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..
Re: [gmx-users] Error No default Proper Dih. types
Dear Justin, thanks for your extra description. Very nice! Last doubt, which values of "phase" and "pn" should I use for [ dihedraltypes ]? Thanks again. Paolo Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul ha scritto: > > > On 4/26/20 2:08 PM, Paolo Costa wrote: > > Dear Justin, > > > > thanks a lot for your quick reply and useful information. > > Thus, I will go through to all the dihedral terms and define zero the > > corresponding force constant as you suggested. In any case, I guess it > will > > be too much work to calculate also the force constant for the torsion > angle > > rotation. > > Metals are usually the bridge point between multiple groups and as such > their dihedrals are all coupled and not generally considered "soft" > (rotatable). So the conformational energetics of these molecules usually > involves only bonds and angles in terms of internal parameters. > > -Justin > > > Thanks again. > > > > Paolo > > > > Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul > ha > > scritto: > > > >> > >> On 4/26/20 1:57 PM, Paolo Costa wrote: > >>> Dear Gromacs users, > >>> > >>> within Amber99 force field I created a new molecule, polyoxometallate, > by > >>> creating a new .rtp file and modifying the atomtypes.atp, > ffnonbonded.itp > >>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters > >>> from known works, while the parameters for the bonding interactions I > >>> determined by Gaussian together with VFFDT software. > >>> I did not insert any parameters for the dihedral angles since the > VFFTDT > >>> software does not calculated them. However as written in the related > >> paper > >>> (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation > >> related > >>> to metals can often be ignored".* > >>> Does somebody knows how to overcome such error in Gromacs? > >> pdb2gmx generates all possible angles and dihedrals, as determined by > >> the bonds that are defined in the .rtp entry. Thus, you likely have > >> dihedrals in the topology in which one of the participating atoms is the > >> metal. You have to have parameters for all defined interactions, but it > >> is true that dihedral terms are not typically used in this case. The > >> simplest solution is to define dihedrals with zero force constants so > >> they do not contribute to the forces in the system. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> == > >> > >> -- > >> 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. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Error No default Proper Dih. types
Dear Justin, thanks a lot for your quick reply and useful information. Thus, I will go through to all the dihedral terms and define zero the corresponding force constant as you suggested. In any case, I guess it will be too much work to calculate also the force constant for the torsion angle rotation. Thanks again. Paolo Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul ha scritto: > > > On 4/26/20 1:57 PM, Paolo Costa wrote: > > Dear Gromacs users, > > > > within Amber99 force field I created a new molecule, polyoxometallate, by > > creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp > > and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters > > from known works, while the parameters for the bonding interactions I > > determined by Gaussian together with VFFDT software. > > I did not insert any parameters for the dihedral angles since the VFFTDT > > software does not calculated them. However as written in the related > paper > > (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation > related > > to metals can often be ignored".* > > Does somebody knows how to overcome such error in Gromacs? > > pdb2gmx generates all possible angles and dihedrals, as determined by > the bonds that are defined in the .rtp entry. Thus, you likely have > dihedrals in the topology in which one of the participating atoms is the > metal. You have to have parameters for all defined interactions, but it > is true that dihedral terms are not typically used in this case. The > simplest solution is to define dihedrals with zero force constants so > they do not contribute to the forces in the system. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
[gmx-users] Error No default Proper Dih. types
Dear Gromacs users, within Amber99 force field I created a new molecule, polyoxometallate, by creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters from known works, while the parameters for the bonding interactions I determined by Gaussian together with VFFDT software. I did not insert any parameters for the dihedral angles since the VFFTDT software does not calculated them. However as written in the related paper (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation related to metals can often be ignored".* Does somebody knows how to overcome such error in Gromacs? Thanks a lot. Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
[gmx-users] Fatal error pdb2gmx
Dear Gromax users, I created a new residue of 118 atoms within Amber99 force field. However when I run the "pdb2gmx" I got many times the following warning: "*WARNING: Duplicate line found in or between hackblock and rtp entries" *and in the end I got the following fatal error: "*Atom O10 in residue POM 0 was not found in rtp entry POM with 118 atoms while sorting atoms*". I have no idea what the warning means, however I do not understand the fatal error since I am sure that the Atom O1 is present in the residue I created. In attachment you can find the .pdb and the .rtp files I created. Please, can somebody figure out what cause such errors? Thanks a lot. Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Problem C-H bonds of Benzene after minimization
Hi Justin, indeed there are only six bonds in the topology files! As you said the hydrogen nomenclature in .rtp file is wrong. Thanks a lot! Paolo Il giorno gio 23 apr 2020 alle ore 12:55 Justin Lemkul ha scritto: > > > On 4/23/20 6:52 AM, Paolo Costa wrote: > > Dear Gromacs Users, > > > > I am trying to perform MD simulations of benzene molecule in a cube of > > water just for practicing. > > By following the tutorial > > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I > setup > > the residue Benzene within Amber99 force field. After the minimization > > however I got the C-H bonds of benzene distorted and unusually stretched. > > During the grompp procedure I got the following note: > > > > " In moleculetype 'Other' 6 atoms are not bound by a potential or > >constraint to any other atom in the same moleculetype. Although > >technically this might not cause issues in a simulation, this often > means > >that the user forgot to add a bond/potential/constraint or put > multiple > >molecules in the same moleculetype definition by mistake. Run with -v > to > >get information for each atom." > > > > Could it be related to the problem I am facing? > > > > Here the starting .pdb file of benzene: > > COMPNDBENZENE > > REMARK1 File created by GaussView 6.0.16 > > HETATM1 C1 C6H6 0 0.968 1.903 0.000 >C > > HETATM2 C2 C6H6 0 2.363 1.903 0.000 >C > > HETATM3 C3 C6H6 0 3.060 3.111 0.000 >C > > HETATM4 C4 C6H6 0 2.363 4.319 -0.001 >C > > HETATM5 C5 C6H6 0 0.968 4.319 -0.002 >C > > HETATM6 C6 C6H6 0 0.270 3.111 -0.001 >C > > HETATM7 H1 C6H6 0 0.418 0.951 0.000 >H > > HETATM8 H2 C6H6 0 2.912 0.951 0.001 >H > > HETATM9 H3 C6H6 0 4.160 3.111 0.001 >H > > HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 >H > > HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 >H > > HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 >H > > END > > CONECT1267 > > CONECT2138 > > CONECT3249 > > CONECT435 10 > > CONECT546 11 > > CONECT615 12 > > CONECT71 > > CONECT82 > > CONECT93 > > CONECT 104 > > CONECT 115 > > CONECT 126 > > > > Here the .rtp file included in Amber99.ff: > > [ C6H6 ] > > [ atoms ] > > C1 CA -0.1285 1 > > C2 CA -0.1285 2 > > C3 CA -0.1285 3 > > C4 CA -0.1285 4 > > C5 CA -0.1285 5 > > C6 CA -0.1285 6 > > H1 HA0.1285 7 > > H2 HA0.1285 8 > > H3 HA0.1285 9 > > H4 HA0.1285 10 > > H5 HA0.1285 11 > > H6 HA0.1285 12 > > [ bonds ] > > C1 H7 > > C1 C2 > > C1 C6 > > C2 C8 > > C2 C1 > > C2 C3 > > C3 H9 > > C3 C2 > > C3 C4 > > C4 H10 > > C4 C3 > > C4 C5 > > C5 H11 > > C5 C4 > > C5 C6 > > C6 H12 > > C6 C5 > > C6 C1 > > > > Can somebody help me to figure out such issue? > > The bonds in the .rtp file are wrong. The hydrogen nomenclature is > incorrect so you do not have any C-H bonds in the topology. You can > verify this for yourself. You probably have 6 bonds instead of 12. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
[gmx-users] Problem C-H bonds of Benzene after minimization
Dear Gromacs Users, I am trying to perform MD simulations of benzene molecule in a cube of water just for practicing. By following the tutorial https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/, I setup the residue Benzene within Amber99 force field. After the minimization however I got the C-H bonds of benzene distorted and unusually stretched. During the grompp procedure I got the following note: " In moleculetype 'Other' 6 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom." Could it be related to the problem I am facing? Here the starting .pdb file of benzene: COMPNDBENZENE REMARK1 File created by GaussView 6.0.16 HETATM1 C1 C6H6 0 0.968 1.903 0.000 C HETATM2 C2 C6H6 0 2.363 1.903 0.000 C HETATM3 C3 C6H6 0 3.060 3.111 0.000 C HETATM4 C4 C6H6 0 2.363 4.319 -0.001 C HETATM5 C5 C6H6 0 0.968 4.319 -0.002 C HETATM6 C6 C6H6 0 0.270 3.111 -0.001 C HETATM7 H1 C6H6 0 0.418 0.951 0.000 H HETATM8 H2 C6H6 0 2.912 0.951 0.001 H HETATM9 H3 C6H6 0 4.160 3.111 0.001 H HETATM 10 H4 C6H6 0 2.913 5.272 -0.001 H HETATM 11 H5 C6H6 0 0.418 5.272 -0.003 H HETATM 12 H6 C6H6 0 -0.829 3.111 -0.001 H END CONECT1267 CONECT2138 CONECT3249 CONECT435 10 CONECT546 11 CONECT615 12 CONECT71 CONECT82 CONECT93 CONECT 104 CONECT 115 CONECT 126 Here the .rtp file included in Amber99.ff: [ C6H6 ] [ atoms ] C1 CA -0.1285 1 C2 CA -0.1285 2 C3 CA -0.1285 3 C4 CA -0.1285 4 C5 CA -0.1285 5 C6 CA -0.1285 6 H1 HA0.1285 7 H2 HA0.1285 8 H3 HA0.1285 9 H4 HA0.1285 10 H5 HA0.1285 11 H6 HA0.1285 12 [ bonds ] C1 H7 C1 C2 C1 C6 C2 C8 C2 C1 C2 C3 C3 H9 C3 C2 C3 C4 C4 H10 C4 C3 C4 C5 C5 H11 C5 C4 C5 C6 C6 H12 C6 C5 C6 C1 Can somebody help me to figure out such issue? Thanks. Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
It was a typos. In the .pdb file I wrote SnC as residue name, while in .rtp file it was still written SnCl. That's why the error. Thanks a lot again. Paolo Il dom 19 apr 2020, 22:05 Justin Lemkul ha scritto: > > > On 4/19/20 3:47 PM, Paolo Costa wrote: > > Hi Justin, > > > > I could fix the issue. > > > > Thanks again for your help. > > And in the spirit of helping others that use this mailing list, what > exactly was the problem and how did you solve it? > > -Justin > > > Paolo > > > > Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul > ha > > scritto: > > > >> > >> On 4/17/20 5:25 PM, Paolo Costa wrote: > >>> Hi Justin, > >>> > >>> thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my > >>> stannate.pdb and also to stannate.rtp. But still I get the error. > >>> Here the output file of from pdb2gmx: > >>> > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.r2b > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b > >>> Reading stannate.pdb... > >>> WARNING: all CONECT records are ignored > >>> Read 'stannate', 7 atoms > >>> Analyzing pdb file > >>> Splitting chemical chains based on TER records or chain id changing. > >>> There are 1 chains and 0 blocks of water and 1 residues with 7 atoms > >>> > >>> chain #res #atoms > >>> 1 ' ' 1 7 > >>> > >>> All occupancy fields zero. This is probably not an X-Ray structure > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/atomtypes.atp > >>> Atomtype 68 > >>> Reading residue database... (amber99) > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.rtp > >>> Residue 93 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp > >>> Residue 94 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp > >>> Residue 110 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp > >>> Residue 126 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp > >>> Residue 127 > >>> Sorting it all out... > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.hdb > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb > >>> Opening force field file > >> /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb > >>> Opening force field file > >> /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb > >>> Back Off! I just backed up topol.top to ./#topol.top.19# > >>> Processing chain 1 (7 atoms, 1 residues) > >>> > >>> Warning: Starting residue SnC0 in chain not identified as > >> Protein/RNA/DNA. > >>> This chain lacks identifiers, which makes it impossible to do strict > >>> classification of the start/end residues. Here we need to guess this > >> residue > >>> should not be part of the chain and instead introduce a break, but that > >> will > >>> be catastrophic if they should in fact be linked. Please check your > >>> structure, > >>> and add SnC to residuetypes.dat if this was not correct. > >>> > >>> Problem with chain definition, or missing terminal residues. > >>> This chain does not appear to contain a recognized chain molecule. > >>> If this is incorrect, you can edit residuetypes.dat to modify the > >> behavior. > >>> 8 out of 8 lines of specbond.dat converted successfully > >>> > >>> --- > >>> Program: gmx pdb2gmx, version 2018.1 > >>> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) > >>> > >>> Fatal error: > >>> Residue 'SnC' not found in residue topology database > >>> > >>> *Thanks a lot for helping!* > >> Without seeing the contents of the PDB file and stannate.rtp, there's > >> not much to go on here. > >> > >>
Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
Hi Justin, I could fix the issue. Thanks again for your help. Paolo Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul ha scritto: > > > On 4/17/20 5:25 PM, Paolo Costa wrote: > > Hi Justin, > > > > thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my > > stannate.pdb and also to stannate.rtp. But still I get the error. > > Here the output file of from pdb2gmx: > > > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b > > Reading stannate.pdb... > > WARNING: all CONECT records are ignored > > Read 'stannate', 7 atoms > > Analyzing pdb file > > Splitting chemical chains based on TER records or chain id changing. > > There are 1 chains and 0 blocks of water and 1 residues with 7 atoms > > > >chain #res #atoms > >1 ' ' 1 7 > > > > All occupancy fields zero. This is probably not an X-Ray structure > > Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp > > Atomtype 68 > > Reading residue database... (amber99) > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp > > Residue 93 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp > > Residue 94 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp > > Residue 110 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp > > Residue 126 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp > > Residue 127 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb > > Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb > > Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb > > > > Back Off! I just backed up topol.top to ./#topol.top.19# > > Processing chain 1 (7 atoms, 1 residues) > > > > Warning: Starting residue SnC0 in chain not identified as > Protein/RNA/DNA. > > This chain lacks identifiers, which makes it impossible to do strict > > classification of the start/end residues. Here we need to guess this > residue > > should not be part of the chain and instead introduce a break, but that > will > > be catastrophic if they should in fact be linked. Please check your > > structure, > > and add SnC to residuetypes.dat if this was not correct. > > > > Problem with chain definition, or missing terminal residues. > > This chain does not appear to contain a recognized chain molecule. > > If this is incorrect, you can edit residuetypes.dat to modify the > behavior. > > 8 out of 8 lines of specbond.dat converted successfully > > > > --- > > Program: gmx pdb2gmx, version 2018.1 > > Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) > > > > Fatal error: > > Residue 'SnC' not found in residue topology database > > > > *Thanks a lot for helping!* > > Without seeing the contents of the PDB file and stannate.rtp, there's > not much to go on here. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
Hi Justin, thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my stannate.pdb and also to stannate.rtp. But still I get the error. Here the output file of from pdb2gmx: Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b Reading stannate.pdb... WARNING: all CONECT records are ignored Read 'stannate', 7 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 7 atoms chain #res #atoms 1 ' ' 1 7 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp Atomtype 68 Reading residue database... (amber99) Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp Residue 93 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp Residue 94 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp Residue 110 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp Residue 126 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp Residue 127 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.19# Processing chain 1 (7 atoms, 1 residues) Warning: Starting residue SnC0 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add SnC to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) Fatal error: Residue 'SnC' not found in residue topology database *Thanks a lot for helping!* Paolo Il giorno ven 17 apr 2020 alle ore 22:55 Justin Lemkul ha scritto: > On Fri, Apr 17, 2020 at 4:50 PM Paolo Costa > wrote: > > > Dear GROMACS user, > > > > I am aware that such error occurs frequently for new users as I am. > > I am learning how to add new residue in Gromacs; I tried first following > a > > tutorial ( > > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) > > and later by creating a benzene, C6H6 molecule, using amber99.ff force > > field. Everything goes fine without any problems. > > > > For the next step I tried to create residue for a molecule, SnCl6, for > > which there are no parameters (just for training). Thus, within > amber99.ff, > > I add in the atomtypes.atp the atom Sn with the corresponding mass (the > Cl > > (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ > > parameters for Sn (again for Cl there are already present). Finally I add > > in ffbonded.itp the parameters for bond stretch and angle (I calculated > > them by Gaussian and VFFDT software). > > > > I created *my .pdb file* as following: > > COMPNDstannate > > REMARK1 File created by GaussView 6.0.16 > > HETATM1 Sn SnCl6 0 0.000 0.000 0.000 > > Sn > > HETATM2 Cl1 SnCl6 0 -0.000 0.000 2.502 > > Cl > > HETATM3 Cl2 SnCl6 0 -0.000 2.502 -0.000 > > Cl > > HETATM4 Cl3 SnCl6 0 2.502 0.000 0.000 > > Cl > > HETATM5 Cl4 SnCl6 0 -0.000 -2.502 0.000 > > Cl > > HETATM6 Cl5 SnCl6 0 -2.502 0.000 -0.000 > > Cl > > HETATM7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 > > Cl > > END > > CONECT12345 > > CONECT167 > > CONECT21 > > CONECT31 > > CONECT41 > > CONECT51 > > CONECT61 > > CONECT71 > > > > > > and *the .rtp file* which I add in the amber99.ff fol
[gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
Dear GROMACS user, I am aware that such error occurs frequently for new users as I am. I am learning how to add new residue in Gromacs; I tried first following a tutorial (https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) and later by creating a benzene, C6H6 molecule, using amber99.ff force field. Everything goes fine without any problems. For the next step I tried to create residue for a molecule, SnCl6, for which there are no parameters (just for training). Thus, within amber99.ff, I add in the atomtypes.atp the atom Sn with the corresponding mass (the Cl (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ parameters for Sn (again for Cl there are already present). Finally I add in ffbonded.itp the parameters for bond stretch and angle (I calculated them by Gaussian and VFFDT software). I created *my .pdb file* as following: COMPNDstannate REMARK1 File created by GaussView 6.0.16 HETATM1 Sn SnCl6 0 0.000 0.000 0.000 Sn HETATM2 Cl1 SnCl6 0 -0.000 0.000 2.502 Cl HETATM3 Cl2 SnCl6 0 -0.000 2.502 -0.000 Cl HETATM4 Cl3 SnCl6 0 2.502 0.000 0.000 Cl HETATM5 Cl4 SnCl6 0 -0.000 -2.502 0.000 Cl HETATM6 Cl5 SnCl6 0 -2.502 0.000 -0.000 Cl HETATM7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 Cl END CONECT12345 CONECT167 CONECT21 CONECT31 CONECT41 CONECT51 CONECT61 CONECT71 and *the .rtp file* which I add in the amber99.ff folder: [ SnCl6 ] [ atoms ] SnSn1.2468 1 Cl1 Cl -0.5411 2 Cl2 Cl -0.5411 3 Cl3 Cl -0.5411 4 Cl4 Cl -0.5411 5 Cl5 Cl -0.5411 6 Cl6 Cl -0.5411 7 [ bonds ] Sn Cl1 Sn Cl2 Sn Cl3 Sn Cl4 Sn Cl5 Sn Cl6 However, although to my eyes I did everything OK, I get such error. *Please, can somebody help me to figure out where I am doing wrong? * Thanks a lot in advance. Paolo Costa -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
Re: [gmx-users] Problem force constant bond stretc.
Thanks a lot. Best regards, Paolo Il giorno gio 16 apr 2020 alle ore 07:57 David van der Spoel < sp...@xray.bmc.uu.se> ha scritto: > Den 2020-04-15 kl. 23:48, skrev Paolo Costa: > > Dear Gromacs users, > > > > I have a problem regarding force constant for bond stretching. By > employing > > VFFDT software, I got C-C bond stretching force constant (for Benzene, > > B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to > > 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of > > Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It > > seems that the value I got from VFFDT is somehow half than the one > reported > > in Amber force field. > > Can somebody help me to figure out such issue? > > > > Thanks a lot in advance for your help. > > > Vbond = (k/2) (r - r0)^2 > > Some methods do not use the division by two, so it can be a matter of > definition. > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.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? 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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
[gmx-users] Problem force constant bond stretc.
Dear Gromacs users, I have a problem regarding force constant for bond stretching. By employing VFFDT software, I got C-C bond stretching force constant (for Benzene, B3LYP-6311++G*) equal to 383.23 kcal/ (mol A^2) which is equivalent to 160343 kj/ (mol nm^2). However when I look to the ffbonded.itp file of Amber99.ff the CA-CA force constant value is 392459.2 kj/ (mol nm^2). It seems that the value I got from VFFDT is somehow half than the one reported in Amber force field. Can somebody help me to figure out such issue? Thanks a lot in advance for your help. -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
[gmx-users] Parametrization POM molecule
Dear Gromacs users, I am new on Gromacs and in general on MD simulations. I am interested on simulating a POM (polyoxometallate) molecule in a water box. I could already find in literature works dealing with POM: - J. Phys. Chem. A 2005, 109, 1216-1222, Phys. Chem. Chem. Phys., 2008, 10, 6940–6953, J Comput Chem 32: 240–247, 2011, Chem. Eur. J. 2016, 22, 15280 – 15289. By looking on those works, I could easily find the Lennard Jones parameters for the non bonded interactions. *However, I could not find the parameters for the bonded interactions.* Do I need such parameters? In case, how can I find them? Because by looking to this paper, Chem. Eur. J. 2016, 22, 15280 – 15289, I will likely use AMBER99 force field which it does not include any parameters for such "exotic" molecule. Thanks a lot. Paolo -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
