Re: [gmx-users] Quick question: is TIP3P water model available in GROMOS54a7 force field?
Hi Shakira and Dr. Lemkul, Thank you so much for your reply! I ended up using an AMBER force field. Best, Wei-Tse On Mon, Apr 27, 2020 at 7:32 PM Justin Lemkul wrote: > > > On 4/27/20 7:43 PM, shakira shukoor wrote: > > Hi > > As far as I know tip3p water model is modelled to use in combination with > > CHARMM force field. However there is nothing wrong in using TIP3P in > > combination with GROMOS force field. And u will have both the bonded and > > non bonded parameters of that specific water model in tip3p,itp file > > itself. You don't have to get it from the force field. Instead you have > to > > add this itp file to the defined topology file you are giving. > > GROMOS force fields were parametrized for use with SPC. As far as I > know, no one has demonstrated that the use of TIP3P with GROMOS is valid. > > -Justin > > > On Tue, Apr 28, 2020 at 4:29 AM Wei-Tse Hsu > wrote: > > > >> Dear gmx users, > >> I prepared a topology using Open Forcefiled for my system. To make > GROMACS > >> able to recognize the water molecules and the ions to be added, I need > to > >> include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my > >> topology file (.top file). I was planning to use GROMOS54a7 with TIP3P > >> water model, so I add the following lines to my topology file: > >> > >> ; Include water topology > >> #include "gromos54a7.ff/tip3p.itp" > >> > >> In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the > >> error of " Atomtype OWT3 not found", I later found that OWT3 was not > >> defined in ffnonbonded.itp. I also tried pdb2gmx command using other > system > >> and chose gromos54a7 force field, but there is no option for selecting > >> TIP3P water model. Therefore, I wonder if TIP3P water model is actually > not > >> available in GROMOS54a7 force field even if there is a tip3p.itp in > >> gromos54a7.ff. I might just use SPC water model instead, but I want to > make > >> sure that my understanding is correct. Thank you! > >> > >> Best, > >> Wei-Tse > >> -- > >> 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://secure-web.cisco.com/1jiuLNgPYje4gVKYOwViv436SLC3KS0A2GQwla3f8JpjGb7IV9SzlFLXlLGZA5gp1w5hZnD71uDp7nseGks0eUee-C_sO3BnHnkKJb1RTW8pA3R4KJKyttkgJE4rApHLqTNRTmyfwLL4LwDMRo7tFjQiwv-Lz1uuAeT3YP3I2wQmHIkzyvdt5DI0J8yjnzYn2fXHdb17TED8np43r3As0cbEwVyhXW_dsYWauCdHP8zD9B7S8ns0sswKvrUpQFmIP16R2mJqEPbG2m5PvhLjPlrVfY1f2JRkpewMmkKabaZxGO0y-Pd8Ml7Vfs_7xuRzpYcyFu36gV2-gs2Qk_kaD51H40RlnXzy_0PIF-z3bdpMVVB3olCx6kZdhF7q6lwSFsc5_8msPUlLROg-REP9rnvj2IGi8HgoHdRE0pBMavNkcCwmQOEqMIlg9_mcsJOwFzCa2TWBKjaLZB0QSjwjxQg/http%3A%2F%2Fwww.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. > > -- 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] Quick question: is TIP3P water model available in GROMOS54a7 force field?
On 4/27/20 7:43 PM, shakira shukoor wrote: Hi As far as I know tip3p water model is modelled to use in combination with CHARMM force field. However there is nothing wrong in using TIP3P in combination with GROMOS force field. And u will have both the bonded and non bonded parameters of that specific water model in tip3p,itp file itself. You don't have to get it from the force field. Instead you have to add this itp file to the defined topology file you are giving. GROMOS force fields were parametrized for use with SPC. As far as I know, no one has demonstrated that the use of TIP3P with GROMOS is valid. -Justin On Tue, Apr 28, 2020 at 4:29 AM Wei-Tse Hsu wrote: Dear gmx users, I prepared a topology using Open Forcefiled for my system. To make GROMACS able to recognize the water molecules and the ions to be added, I need to include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my topology file (.top file). I was planning to use GROMOS54a7 with TIP3P water model, so I add the following lines to my topology file: ; Include water topology #include "gromos54a7.ff/tip3p.itp" In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the error of " Atomtype OWT3 not found", I later found that OWT3 was not defined in ffnonbonded.itp. I also tried pdb2gmx command using other system and chose gromos54a7 force field, but there is no option for selecting TIP3P water model. Therefore, I wonder if TIP3P water model is actually not available in GROMOS54a7 force field even if there is a tip3p.itp in gromos54a7.ff. I might just use SPC water model instead, but I want to make sure that my understanding is correct. Thank you! Best, Wei-Tse -- 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] Quick question: is TIP3P water model available in GROMOS54a7 force field?
Hi As far as I know tip3p water model is modelled to use in combination with CHARMM force field. However there is nothing wrong in using TIP3P in combination with GROMOS force field. And u will have both the bonded and non bonded parameters of that specific water model in tip3p,itp file itself. You don't have to get it from the force field. Instead you have to add this itp file to the defined topology file you are giving. On Tue, Apr 28, 2020 at 4:29 AM Wei-Tse Hsu wrote: > Dear gmx users, > I prepared a topology using Open Forcefiled for my system. To make GROMACS > able to recognize the water molecules and the ions to be added, I need to > include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my > topology file (.top file). I was planning to use GROMOS54a7 with TIP3P > water model, so I add the following lines to my topology file: > > ; Include water topology > #include "gromos54a7.ff/tip3p.itp" > > In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the > error of " Atomtype OWT3 not found", I later found that OWT3 was not > defined in ffnonbonded.itp. I also tried pdb2gmx command using other system > and chose gromos54a7 force field, but there is no option for selecting > TIP3P water model. Therefore, I wonder if TIP3P water model is actually not > available in GROMOS54a7 force field even if there is a tip3p.itp in > gromos54a7.ff. I might just use SPC water model instead, but I want to make > sure that my understanding is correct. Thank you! > > Best, > Wei-Tse > -- > 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. > -- *Best Regards* Shakkira E PhD student INSPIRE Scholar Department of Chemistry sdmdlab.xyz IIT Patna Bihta Patna 801106 -- 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] Quick question: is TIP3P water model available in GROMOS54a7 force field?
Dear gmx users, I prepared a topology using Open Forcefiled for my system. To make GROMACS able to recognize the water molecules and the ions to be added, I need to include itp files (such as tip3p.itp, spc.itp, ions.itp, etc.) in my topology file (.top file). I was planning to use GROMOS54a7 with TIP3P water model, so I add the following lines to my topology file: ; Include water topology #include "gromos54a7.ff/tip3p.itp" In gromos54a7.ff, there is indeed a tip3p.itp file. However, getting the error of " Atomtype OWT3 not found", I later found that OWT3 was not defined in ffnonbonded.itp. I also tried pdb2gmx command using other system and chose gromos54a7 force field, but there is no option for selecting TIP3P water model. Therefore, I wonder if TIP3P water model is actually not available in GROMOS54a7 force field even if there is a tip3p.itp in gromos54a7.ff. I might just use SPC water model instead, but I want to make sure that my understanding is correct. Thank you! Best, Wei-Tse -- 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.
