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...@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. > > > > > > -- > == > > 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 >
Re: [gmx-users] Error No default Proper Dih. types
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 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. -- == 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.
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
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.
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.
Re: [gmx-users] Error No default Proper Dih. types
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.
