[gmx-users] topology files for ligands in MD Simulation under OPLS AA force field
Dear All: I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type of each atom from the ligands? 2, how to define the charges of each atom? I know that, when the atom type is defined, there will be a corresponding charge to this atom type. Does it safe to use this charge in the simulations on the ligands (since these charges are designed for amino acids)? 3,When the atom type and the charge of atom are defined, how to prepare the file in the GROMACS format? Does there easier method to prepare such files than manually? Thank you very much for your time and your kindness. I really appreciate if any one can share their experience in preparing the topology files for ligands used under OPLS_AA force field and GROMACS package. Sincerely Yours Ruo-Xu Gu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] topology files for ligands in MD Simulation under OPLS AA force field
mirc...@sjtu.edu.cn wrote: Dear All: I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type of each atom from the ligands? 2, how to define the charges of each atom? I know that, when the atom type is defined, there will be a corresponding charge to this atom type. Does it safe to use this charge in the simulations on the ligands (since these charges are designed for amino acids)? Proper parameterization is a difficult task. See, for instance: http://www.gromacs.org/Documentation/How-tos/Parameterization 3,When the atom type and the charge of atom are defined, how to prepare the file in the GROMACS format? Does there easier method to prepare such files than manually? There is at least one script (topolgen.pl) in the User Contributions section of the Gromacs site, but it is not terribly intelligent and the resulting topology should not be viewed as something that you should use without proper validation. http://www.gromacs.org/Downloads/User_contributions/Other_software Otherwise, break out Chapter 5 of the manual (something you should probably do anyway) and your favorite text editor. -Justin Thank you very much for your time and your kindness. I really appreciate if any one can share their experience in preparing the topology files for ligands used under OPLS_AA force field and GROMACS package. Sincerely Yours Ruo-Xu Gu -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] topology files for ligands in MD Simulation under OPLS AA force field
mircial at sjtu.edu.cn mircial at sjtu.edu.cn wrote I am using GROMACS package to do molecular dynamics simulations under OPLS_AA force field. I encounter some problems when preparing the topology files of small molecules (ligands).My questions are as follows: 1, how to chose the atom type of each atom from the ligands? amber + GAFF would be easier, here the ligand parameterization is pretty straight forward (there's probably a HOWTO) with OPLS you want to work with homology, and if you don't need any high throughput you can do it manually ... look up groups in amino acids that are similar to your the components of your ligands, and choose the atomtypes accordingly. 2, how to define the charges of each atom? I know that, when the atom type is defined, there will be a corresponding charge to this atom type. Does it safe to use this charge in the simulations on the ligands (since these charges are designed for amino acids)? yes, OPLS was mostly used for peptides, but AFAIK, the original parameterization in Jorgensens group started with generic organic molecules, there's certainly papers from this group that present parameters for non-peptide molecules, e.g., various hetero cycles ... (I am not sure whether the gmx topology folder only contains the part of OPLS relevant for peptides, or all of it, if not ask someone from the Jorgenson group, they might give you the original parameter files) However, if you have some generic organic molecules and assign OPLS atom types there is no guarantee that the charges add up to zero (for a neutral molecule) ... what i did before, with reasonable success, is combine EPSD (SCF or AM1BCC) charges with OPLS parameters... In any case, as has been pointed out before many times in this list mixing different FFs, or using ad-hoc values for some parameters, is dangerous, and you really want to test your molecules before using them in any extensive calculations. A good start might be to compare structures that were minimized with your FF to the same structure minimized at the DFT or MP2 level (HF-SCF might do as well depending on the molecule) ... but that's probably not enough ... 3,When the atom type and the charge of atom are defined, how to prepare the file in the GROMACS format? Does there easier method to prepare such files than manually? As for the bonded interactions, in some cases pdb2gmx and grompp can figure them out by themselves. You'd assign atom- (thereby bond-) types, and the bonds, then make a new entry in the rtp file, including only the atoms and bonds sections. you choose a new 3 letter residue name, and starting from a PDB file of the ligand (with this residue name, and the same atom order and the same atom names as in the rtp entry) use pdb2gmx/grompp. However often enough, especially for proper and improper dihedrals you have to define them manually (again by anlogy) for anything but the simplest molecules its a painstaking task ... so you either take the time, or you use amber (or you talk to Schrodinger, they will have some script for assigning OPLS parameters but that probably wont work with Gromacs) good luck! mic -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
