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 <jalem...@vt.edu> 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 <weitse....@colorado.edu> > 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.