Re: [gmx-users] Re: OPLS-AA/L force field
you zou wrote: Hi, Thank you for your help.Now there is this question that I have just .pdb file and when use protonate command it is protonate -f drg.pdb -o drg.gro, this is without hydrogens atoms too. I think something is wrong, but I don't know what it is.In definition of protonate there is protonate reads (a) conformation(s) and adds all missing hydrogens as defined in ffgmx2.hdb http://rocks5.vki.ac.be/gromacs/online/hdb.html. but I can't add hydrogens. What is my problem? Well, your command isn't correct. The protonate command takes (at minimum) the -s flag, not -f (which is optional, and context-dependent, if I recall). The other fact is that if a residue isn't listed in ffgmx2.hdb, it won't get protonated, but it is trivial to add new molecules into the .hdb file with the help of the manual. The syntax for .hdb entries is straightforward. -Justin Thanks you zou wrote: Hi again, Sorry, I have one question now, what is the meaning of structure? I think coordinates is structure, is it true? Yes, a coordinate file contains a structure. If it is true, when I used editconf -f drg.pdb -o drg.gro number of atoms are different from top file and editconf can not add hydrogens to drg.gro. If Gromacs can handle .pdb, How can it do this, because number of atoms are different(Which command I have to use?). If can't handle it how can I add Hydrogens to drg.gro? The underlying assumption when running any simulation is that you have developed the proper parameters for the ligand and that it has an appropriate structure. If you need additional hydrogens, the Gromacs protonate tool can generate an all-atom structure. -Justin Thanks, you zou wrote: Hi again, Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I use editconf command I will miss something, is it true? If you want to use x2top, the assumption is that the structure is already appropriate as is, that is it is properly protonated. The only tool that is smart enough to add force field-specific hydrogens is pdb2gmx. If you're using OPLS-AA, then you should have all hydrogens present, anyway. If that's true, then you can use editconf to create a .gro file (which is not absolutely necessary; Gromacs can handle .pdb files just fine). If you don't have all the appropriate atoms present in your molecule's structure, then you need to build a proper structure. -Justin Thank you again you zou wrote: 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 ... g t; Program x2top, VERSION 4.0.5 Source code file: x2top.c, line: 207 Fatal error: Could only find a f orcefield type for 6 out of 24 atoms Not all of your atom types are described by ffop lsaa.n2t so you will have to add them. There are only a limited number of types that are covered by default. http://www.gromacs.org/Documentation/File_Formats/.n2t_File 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? Do you just need a .gro file, and not a .top? My understanding from your first message was that you needed a topo logy. If you just need a .gro, then simply pass your .pdb file to editconf. -Justin br 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 gt; 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 c an build the topology by hand. No matter what you choose, you ne ed a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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
Re: [gmx-users] Re: OPLS-AA/L force field
you zou wrote: Hi again, Sorry, I have one question now, what is the meaning of structure? I think coordinates is structure, is it true? Yes, a coordinate file contains a structure. If it is true, when I used editconf -f drg.pdb -o drg.gro number of atoms are different from top file and editconf can not add hydrogens to drg.gro. If Gromacs can handle .pdb, How can it do this, because number of atoms are different(Which command I have to use?). If can't handle it how can I add Hydrogens to drg.gro? The underlying assumption when running any simulation is that you have developed the proper parameters for the ligand and that it has an appropriate structure. If you need additional hydrogens, the Gromacs protonate tool can generate an all-atom structure. -Justin Thanks, you zou wrote: Hi again, Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I use editconf command I will miss something, is it true? If you want to use x2top, the assumption is that the structure is already appropriate as is, that is it is properly protonated. The only tool that is smart enough to add force field-specific hydrogens is pdb2gmx. If you're using OPLS-AA, then you should have all hydrogens present, anyway. If that's true, then you can use editconf to create a .gro file (which is not absolutely necessary; Gromacs can handle .pdb files just fine). If you don't have all the appropriate atoms present in your molecule's structure, then you need to build a proper structure. -Justin Thank you again you zou wrote: 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 ... g t; 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 Not all of your atom types are described by ffoplsaa.n2t so you will have to add them. There are only a limited number of types that are covered by default. http://www.gromacs.org/Documentation/File_Formats/.n2t_File 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? Do you just need a .gro file, and not a .top? My understanding from your first message was that you needed a topo logy. If you just need a .gro, then simply pass your .pdb file to editconf. -Justin 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 gt; 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 ne ed a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 - Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969 -- 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 listgmx-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
Re: [gmx-users] Re: OPLS-AA/L force field
The force fields have to be compatible but this way works fine. On 19 May 2010 12:50, Justin A. Lemkul 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_typemasscharge ptype sigma epsilon CYCY 0. 0. A 3.39967e-01 4.57730e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 O2O2 0. 0. A 2.95992e-01 8.78640e-01 N N 0. 0. A 3.25000e-01 7.11280e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OYOY 0. 0. A 3.1e-01 7.11280e-01 HCHC 0. 0. A 2.64953e-01 6.56888e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 C C 0. 0. A 3.39967e-01 3.59824e-01 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 OHOH 0. 0. A 3.06647e-01 8.80314e-01 #include protein.itpfrom 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.itpfrom 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 fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include Na_amber99sb.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 trisacc1 SOL 10697 Na 4 2010/5/19 you zou 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 listgmx-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
Re: [gmx-users] Re: OPLS-AA/L force field
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_typemasscharge ptype sigma epsilon CYCY 0. 0. A 3.39967e-01 4.57730e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 O2O2 0. 0. A 2.95992e-01 8.78640e-01 N N 0. 0. A 3.25000e-01 7.11280e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OYOY 0. 0. A 3.1e-01 7.11280e-01 HCHC 0. 0. A 2.64953e-01 6.56888e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 C C 0. 0. A 3.39967e-01 3.59824e-01 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 OHOH 0. 0. A 3.06647e-01 8.80314e-01 #include protein.itpfrom 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.itpfrom 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 fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include Na_amber99sb.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 trisacc1 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
Re: [gmx-users] Re: OPLS-AA/L force field
*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_typemasscharge ptype sigma epsilon CYCY 0. 0. A 3.39967e-01 4.57730e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 O2O2 0. 0. A 2.95992e-01 8.78640e-01 N N 0. 0. A 3.25000e-01 7.11280e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OYOY 0. 0. A 3.1e-01 7.11280e-01 HCHC 0. 0. A 2.64953e-01 6.56888e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 C C 0. 0. A 3.39967e-01 3.59824e-01 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 OHOH 0. 0. A 3.06647e-01 8.80314e-01 #include protein.itpfrom 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.itpfrom 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 fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include Na_amber99sb.itp [ system ] ; Name
Re: [gmx-users] Re: OPLS-AA/L force field
*If you are familiar to ambertools (tleap mainly), so you can create your molecule there, save the amber parameters and use acpype to convert from amber to gromacs format. *Thanks Alan, I use tleap and then amb2gmx.pl. It works great, the only problem is the NAc groups aren't restrained properly so have to manually edit them in. I'll have to do some reading about acpype... On 20 May 2010 13:28, Alan alanwil...@gmail.com wrote: Dear Oliver, On Thu, May 20, 2010 at 13:21, gmx-users-requ...@gromacs.org wrote: 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! If you are familiar to ambertools (tleap mainly), so you can create your molecule there, save the amber parameters and use acpype to convert from amber to gromacs format. Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] Re: OPLS-AA/L force field
you zou wrote: 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 Not all of your atom types are described by ffoplsaa.n2t so you will have to add them. There are only a limited number of types that are covered by default. http://www.gromacs.org/Documentation/File_Formats/.n2t_File 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? Do you just need a .gro file, and not a .top? My understanding from your first message was that you needed a topology. If you just need a .gro, then simply pass your .pdb file to editconf. -Justin 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 -- 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 listgmx-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
Re: [gmx-users] Re: OPLS-AA/L force field
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! :) ; ;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_typemasscharge ptype sigma epsilon CYCY 0. 0. A 3.39967e-01 4.57730e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 O2O2 0. 0. A 2.95992e-01 8.78640e-01 N N 0. 0. A 3.25000e-01 7.11280e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OYOY 0. 0. A 3.1e-01 7.11280e-01 HCHC 0. 0. A 2.64953e-01 6.56888e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 C C 0. 0. A 3.39967e-01 3.59824e-01 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 OHOH 0. 0. A 3.06647e-01 8.80314e-01 #include protein.itpfrom 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.itpfrom 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 fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include Na_amber99sb.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 trisacc1 SOL 10697 Na 4 2010/5/19 you zou 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 listgmx-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 listgmx-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
Re: [gmx-users] Re: OPLS-AA/L force field
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_typemasscharge ptype sigma epsilon CYCY 0. 0. A 3.39967e-01 4.57730e-01 O O 0. 0. A 2.95992e-01 8.78640e-01 HOHO 0. 0. A 0.0e+00 0.0e+00 H1H1 0. 0. A 2.47135e-01 6.56888e-02 O2O2 0. 0. A 2.95992e-01 8.78640e-01 N N 0. 0. A 3.25000e-01 7.11280e-01 H2H2 0. 0. A 2.29317e-01 6.56888e-02 OYOY 0. 0. A 3.1e-01 7.11280e-01 HCHC 0. 0. A 2.64953e-01 6.56888e-02 H H 0. 0. A 1.06908e-01 6.56888e-02 C C 0. 0. A 3.39967e-01 3.59824e-01 OSOS 0. 0. A 3.1e-01 7.11280e-01 CGCG 0. 0. A 3.39967e-01 4.57730e-01 OHOH 0. 0. A 3.06647e-01 8.80314e-01 #include protein.itpfrom 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.itpfrom 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 fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include Na_amber99sb.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 trisacc1 SOL 10697 Na 4 2010/5/19 you zou 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 listgmx-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
Re: [gmx-users] Re: OPLS-AA/L force field
you zou wrote: Hi again, Sorry I confused you with my question. My question is How can I make .gro file and .top file from drug.pdb (that removed from drug-enzyme.pdb)? If I can use x2top command I will make .top file just, is it true? I think .gro file is dependent on forcefiled too so If I use editconf command I will miss something, is it true? If you want to use x2top, the assumption is that the structure is already appropriate as is, that is it is properly protonated. The only tool that is smart enough to add force field-specific hydrogens is pdb2gmx. If you're using OPLS-AA, then you should have all hydrogens present, anyway. If that's true, then you can use editconf to create a .gro file (which is not absolutely necessary; Gromacs can handle .pdb files just fine). If you don't have all the appropriate atoms present in your molecule's structure, then you need to build a proper structure. -Justin Thank you again you zou wrote: 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 ... g t; 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 Not all of your atom types are described by ffoplsaa.n2t so you will have to add them. There are only a limited number of types that are covered by default. http://www.gromacs.org/Documentation/File_Formats/.n2t_File 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? Do you just need a .gro file, and not a .top? My understanding from your first message was that you needed a topo logy. If you just need a .gro, then simply pass your .pdb file to editconf. -Justin 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 ne ed a thorough understanding of the mechanics of your chosen force field, methods of validation, and of course Chapter 5 in the Gromacs manual. Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- 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 listgmx-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
