Re: [gmx-users] a99SB-disp forcefield
Yes. E-mail him directly. J On Wed, Jul 3, 2019 at 8:48 AM Timofey Tyugashev wrote: > Paul as Paul Robustelli, the paper author? > > 02.07.2019 17:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: > > Message: 3 > > Date: Tue, 2 Jul 2019 09:52:04 +0200 > > From: Jo?o Henriques > > To:gmx-us...@gromacs.org, "Greener, Joe" > > Subject: Re: [gmx-users] a99SB-disp forcefield > > Message-ID: > >zu-3jypzd3tsxy...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Ask Paul, they have a Gromacs version of it and he'll most likely be > happy > > to share it with you. > > > > J > > > > On Mon, Jul 1, 2019 at 8:19 PM Joe Greener wrote: > > > >> Dear Gromacs users, > >> > >> I am looking to use the a99SB-disp forcefield from Robustelli et al. > >> PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs > 2019.3. > >> > >> The details of the forcefield are in the paper supplementary material. I > >> have carried out the following steps: > >> - Downloaded the Amber99SB*-ILDN-Q forcefield from > >> http://www.gromacs.org/Downloads/User_contributions/Force_fields as > >> ff99sb-star-ildn-q.tgz. > >> - Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz > >> and extracted the water files. > >> - Modified the water parameters to match a99SB-disp and created a > >> pre-equilibrated water box. > >> - Modified the partial charges on certain residues as required. > >> > >> Two steps remain that I could do with some advice on: > >> > >> - The torsion parameters in the paper are given as phi_0, k_1, k_2, ..., > >> k_6. Sometimes k_2 onwards are missing, and values generally range -1.0 > >> to 1.0. I have looked at the list of dihedral types in the Gromacs > >> manual and can't find which type these correspond to, or how to convert > >> the values to a valid dihedral format. I guess this format is the one > >> used by Desmond. > >> - The a99SB-disp forcefield has a non-bonded LJ override between all > >> backbone carbonyl oxygens and amide hydrogens. It seems I could have an > >> entry something like this in the forcefield files: > >> > >> [ nonbond_params ] > >> O H1sigma_val epsilon_val > >> > >> Would this be sufficient to add this constraint? > >> > >> Has anyone else tried to implement the a99SB-disp forcefield in Gromacs? > >> If not I'm happy to make it available if I get it working. > >> > >> Best, > >> Joe > >> > >> Joe Greener > >> Research Associate, UCL > >> http://jgreener64.github.io/ > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Readhttp://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 togmx-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? 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? 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] a99SB-disp forcefield
Paul as Paul Robustelli, the paper author? 02.07.2019 17:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: Message: 3 Date: Tue, 2 Jul 2019 09:52:04 +0200 From: Jo?o Henriques To:gmx-us...@gromacs.org, "Greener, Joe" Subject: Re: [gmx-users] a99SB-disp forcefield Message-ID: Content-Type: text/plain; charset="UTF-8" Ask Paul, they have a Gromacs version of it and he'll most likely be happy to share it with you. J On Mon, Jul 1, 2019 at 8:19 PM Joe Greener wrote: Dear Gromacs users, I am looking to use the a99SB-disp forcefield from Robustelli et al. PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3. The details of the forcefield are in the paper supplementary material. I have carried out the following steps: - Downloaded the Amber99SB*-ILDN-Q forcefield from http://www.gromacs.org/Downloads/User_contributions/Force_fields as ff99sb-star-ildn-q.tgz. - Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz and extracted the water files. - Modified the water parameters to match a99SB-disp and created a pre-equilibrated water box. - Modified the partial charges on certain residues as required. Two steps remain that I could do with some advice on: - The torsion parameters in the paper are given as phi_0, k_1, k_2, ..., k_6. Sometimes k_2 onwards are missing, and values generally range -1.0 to 1.0. I have looked at the list of dihedral types in the Gromacs manual and can't find which type these correspond to, or how to convert the values to a valid dihedral format. I guess this format is the one used by Desmond. - The a99SB-disp forcefield has a non-bonded LJ override between all backbone carbonyl oxygens and amide hydrogens. It seems I could have an entry something like this in the forcefield files: [ nonbond_params ] O H1sigma_val epsilon_val Would this be sufficient to add this constraint? Has anyone else tried to implement the a99SB-disp forcefield in Gromacs? If not I'm happy to make it available if I get it working. Best, Joe Joe Greener Research Associate, UCL http://jgreener64.github.io/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Readhttp://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 togmx-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? 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] a99SB-disp forcefield
Ask Paul, they have a Gromacs version of it and he'll most likely be happy to share it with you. J On Mon, Jul 1, 2019 at 8:19 PM Joe Greener wrote: > Dear Gromacs users, > > I am looking to use the a99SB-disp forcefield from Robustelli et al. > PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3. > > The details of the forcefield are in the paper supplementary material. I > have carried out the following steps: > - Downloaded the Amber99SB*-ILDN-Q forcefield from > http://www.gromacs.org/Downloads/User_contributions/Force_fields as > ff99sb-star-ildn-q.tgz. > - Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz > and extracted the water files. > - Modified the water parameters to match a99SB-disp and created a > pre-equilibrated water box. > - Modified the partial charges on certain residues as required. > > Two steps remain that I could do with some advice on: > > - The torsion parameters in the paper are given as phi_0, k_1, k_2, ..., > k_6. Sometimes k_2 onwards are missing, and values generally range -1.0 > to 1.0. I have looked at the list of dihedral types in the Gromacs > manual and can't find which type these correspond to, or how to convert > the values to a valid dihedral format. I guess this format is the one > used by Desmond. > - The a99SB-disp forcefield has a non-bonded LJ override between all > backbone carbonyl oxygens and amide hydrogens. It seems I could have an > entry something like this in the forcefield files: > > [ nonbond_params ] > O H1sigma_val epsilon_val > > Would this be sufficient to add this constraint? > > Has anyone else tried to implement the a99SB-disp forcefield in Gromacs? > If not I'm happy to make it available if I get it working. > > Best, > Joe > > Joe Greener > Research Associate, UCL > http://jgreener64.github.io/ > > -- > 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? 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] a99SB-disp forcefield
Dear Gromacs users, I am looking to use the a99SB-disp forcefield from Robustelli et al. PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3. The details of the forcefield are in the paper supplementary material. I have carried out the following steps: - Downloaded the Amber99SB*-ILDN-Q forcefield from http://www.gromacs.org/Downloads/User_contributions/Force_fields as ff99sb-star-ildn-q.tgz. - Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz and extracted the water files. - Modified the water parameters to match a99SB-disp and created a pre-equilibrated water box. - Modified the partial charges on certain residues as required. Two steps remain that I could do with some advice on: - The torsion parameters in the paper are given as phi_0, k_1, k_2, ..., k_6. Sometimes k_2 onwards are missing, and values generally range -1.0 to 1.0. I have looked at the list of dihedral types in the Gromacs manual and can't find which type these correspond to, or how to convert the values to a valid dihedral format. I guess this format is the one used by Desmond. - The a99SB-disp forcefield has a non-bonded LJ override between all backbone carbonyl oxygens and amide hydrogens. It seems I could have an entry something like this in the forcefield files: [ nonbond_params ] O H 1 sigma_val epsilon_val Would this be sufficient to add this constraint? Has anyone else tried to implement the a99SB-disp forcefield in Gromacs? If not I'm happy to make it available if I get it working. Best, Joe Joe Greener Research Associate, UCL http://jgreener64.github.io/ -- 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.
