*I guess that depends on what you mean by "works fine." * I mean the method of using pdb2gmx to generate a top and gro and then appending the gro files and including the .itp files in the .top file, works if you want to use two force fields. Originally I thought that was the question.
*I guess it all depends on what you mean (below) by "non amber force field"* I'm using GLYCAM06, so it involves a bit more effort to generate a .top and .gro file than just using pdb2gmx but I thought I'd leave it out as I just wanted to explain the method I use to include it. Apologies for the confusion! Oliver -Justin On 20 May 2010 13:00, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Oliver Grant wrote: > >> The force fields have to be compatible but this way works fine. >> >> > I guess that depends on what you mean by "works fine." If you mean that > you can produce a stable simulation, then yes, it may "work," but I would > question the underlying premise of combining different force fields. If, > for example, you're using an AMBER force field for, say, a protein, and OPLS > for a small molecule, then what you're doing is wrong. The combination > rules required by both force fields are different, as are the underlying > derivation schemes and quite possibly some more details I'm not thinking > about at the moment. > > I guess it all depends on what you mean (below) by "non amber force field" > and how different it is from the actual requirements of the AMBER force > field you're using. If this "non amber force field" was designed to be > compatible with your chosen force field, and there was some suitable > derivation scheme involved, then things will probably work. If you're > mixing and matching parameter sets, be prepared for very tough questions > from any reviewers who see your work. > > -Justin > > On 19 May 2010 12:50, Justin A. Lemkul <jalem...@vt.edu <mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Oliver Grant wrote: >> >> Can you not run pdb2gmx for each of your molecules that you want >> separate force fields for? Then cat the gro files, renumber and >> include the molecule types as .itp files in the .top file as >> below. If I'm doing anything wrong please let me know! :) >> >> >> Combining different force fields into a single system completely >> invalidates it, so yes, I'd say you're doing something wrong :) >> >> -Justin >> >> >> ; >> ; This is your topology file >> >> ; "What If None Of Your Dreams Come True ?" (E. Costello) >> ; >> ; Include forcefield parameters >> #include "ffamber99sb.itp" >> >> [ atomtypes ] >> >> >> ------------------------------------------------------------------------------------from >> the top file of the non amber force field >> ;name bond_type mass charge ptype sigma >> epsilon >> CY CY 0.0000 0.0000 A 3.39967e-01 4.57730e-01 >> O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01 >> HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00 >> H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02 >> O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01 >> N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01 >> H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02 >> OY OY 0.0000 0.0000 A 3.00001e-01 7.11280e-01 >> HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02 >> H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02 >> C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01 >> OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01 >> CG CG 0.0000 0.0000 A 3.39967e-01 4.57730e-01 >> OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01 >> >> #include >> >> >> "protein.itp"------------------------------------------------------------------------------------from >> the top file of the amber force field, contains everything >> usually specified here under [molecule types]. >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> #ifdef POSRES_CA >> #include "CA_posre.itp" >> #endif >> >> #include >> >> >> "trisacc.itp"------------------------------------------------------------------------------------from >> the top file of the non amber force field, contains charges etc. >> >> ; Include Position restraint file >> #ifdef POSRES_trisacc >> #include "trisacc_posre.itp" >> #endif >> >> ; Include water topology >> #include "ffamber_tip3p.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcx fcy fcz >> 1 1 1000 1000 1000 >> #endif >> >> ; Include generic topology for ions >> #include "Na_amber99sb.itp" >> >> [ system ] >> ; Name >> Protein in water >> >> [ molecules ] >> ; Compound #mols >> Protein_A 1 >> trisacc 1 >> SOL 10697 >> Na 4 >> >> >> >> 2010/5/19 you zou <zou....@live.com <mailto:zou....@live.com> >> <mailto:zou....@live.com <mailto:zou....@live.com>>> >> >> >> >> Hi Justin, >> >> Thank you for your help, But when I run x2top command there >> is one >> error that is: >> " >> Can not find forcefield for atom C1-1 with 2 bonds >> Can not find forcefield for atom C4-4 with 2 bonds >> ... >> Program x2top, VERSION 4.0.5 >> Source code file: x2top.c, line: 207 >> >> Fatal error: >> Could only find a forcefield type for 6 out of 24 atoms" >> >> I don't know how can I adjust this error. >> I have one more question again, this command give me a top >> file, if >> I want gro file of this pdb (drug that has removed from >> drug-enzyme >> complex) how can I do that? >> >> you zou wrote: >> > Dear Users, >> > > I have one question about Drug-Enzyme Complex,Similar >> to tutorial If I >> >> > >> want to use GROMOS96 43a1, I can use "Prodrg Beta version" >> for drug > but If I want to use OPLS-AA/L all-atom force >> field I can use "Prodrg > Beta version" server too, or not? >> >> No. You can't use two different force fields in one >> simulation system. >> >> >> >> > If I can't use this server, how can I make .gro file and >> .itp file for > drug that remove from initial .pdb file? >> > >> There are several programs in the User Contributions from the >> website, x2top >> >> (which is distributed with Gromacs), or you can build the >> topology by hand. No matter what you choose, you need a >> thorough understanding of the mechanics of your chosen force >> field, methods of validation, and of course Chapter 5 in the >> >> Gromacs manual. >> >> >> Thanks >> >> >> >> ------------------------------------------------------------------------ >> Hotmail: Free, trusted and rich email service. Get it now. >> <https://signup.live.com/signup.aspx?id=60969> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
