> Thanks, and I accept your suggestions; > > If SwissParam was designed to be used with CHARMM, the most intuitive next > step is to use CHARMM for the MD, is it not?I understand the point about > trying to keep the force fields consistent between docking and MD, but it > may not be feasible (i.e., there may not be suitable parameters in OPLS for > the bizarre functional groups you're dealing with). > > Yes, I also tried CHARMM FF to generate the topology file of the protein > using pdb2gmx (without ligand), and as per the swissparam and gromacs > tutorial i could build the protein-ligand-lipid bilayer and minimize it > using mdrun and and i am at the NPT equilibration step, everything is ok > with this procedure and without errors, but my lipid bilayer is made up of > POPC and the POPC itp file has OPLS FF topologies. So, i was wondering > whether the POPC itp file i am using for MD simulations can be used with the > protein and ligand topology file generated by CHARMM. > > and as per the swissparam tutorial the command to generate topology file > for protein is: > > pdb2gmx -f protein.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb > -nochargegrp > > > > in the gromacs 4.5.4 version the option to select Charmm FF from the > pdb2gmx command is available, but i could not understand the usage of > -nochargegp flag as per the tutorial, is this flag still valid while > generating toplogies. > > Please let me know your comments and suggestions regarding the procedure > followed and the itp files usage for gromacs MD simulations. > > Thanks in advance, > > Pramod > > > > On Wed, Oct 12, 2011 at 3:10 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > >> >> >> ram bio wrote: >> >>> Dear Justin, >>> >>> As i generated the protein-ligand docked complex using opls FF, for the >>> consistency, i am trying to use opls ff generated ligand parameters during >>> md simulations in lipid bi layer. I found that MKTOP can generate topology >>> files using opls ff for small molecules. >>> >>> >> I understand that. The program did a poor job, per the reasons I cited >> before. I do not know anything about mktop (other than what it does), so I >> cannot analyze its suitability here, but due to missing parameters and bogus >> charges, you should not use that topology for anything. >> >> >> I have also tried swiss param to generate the ligand parameters to be >>> used in protein ligand simulation using gromacs. The force field i am using >>> for simulations is OPLS. My ligand contains an azido group and a tropane >>> ring with protonated nitrogen. SwissParam force field has been designed to >>> be compatible with the Charmm force field, but they are not tested on >>> opls.Using the ligand topologies from swissparam, i was able to run the MD >>> simulations using gromacs with opls without errors (swissparam - gromacs >>> tutorial), only issues being the charges on the ligand, so i generated >>> various input files (mol2 files) for swissparam with charges generated >>> using ambcc1, gastergier and MMFF. But the itp files obtained from >>> swissparam had same charges for the ligand atoms irrespective of the input >>> provided i.e. charged or uncharged mol2 files, and >>> >>> >> If SwissParam was designed to be used with CHARMM, the most intuitive next >> step is to use CHARMM for the MD, is it not? I understand the point about >> trying to keep the force fields consistent between docking and MD, but it >> may not be feasible (i.e., there may not be suitable parameters in OPLS for >> the bizarre functional groups you're dealing with). >> >> As per Gromacs website: >>> >>> "Note that an .itp file <http://www.gromacs.org/** >>> Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>> >>> will be specific to a given force field, and will only function when >>> included by a .top file <http://www.gromacs.org/** >>> Documentation/File_Formats/.**top_File<http://www.gromacs.org/Documentation/File_Formats/.top_File>> >>> that has previously included the .itp files <http://www.gromacs.org/** >>> Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>> >>> for that force field. Appropriate use of the |#define| and |#ifdef| >>> mechanisms can permit the same .itp file <http://www.gromacs.org/** >>> Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File>> >>> to work with multiple force fields, e.g. |share/top/water.itp|." >>> >>> >> Note the key caveat here - through the use of #define and #ifdef you can >> make use of different force fields. That means you can control which >> parameters are applied based on different conditions. I could write an .itp >> file for any molecule that has force field parameters for any force field, >> and all I'd have to do is enclose all relevant directives within #ifdef >> blocks and it would work. This note does *not* indicate that you can mix >> and match force fields. Doing so is generally a very bad idea, if it even >> works syntactically. >> >> >> so, i think even though the swissparam generated topologies based on MMFF >>> fit to charmm (based on testing), they could also be used with opls. It was >>> informed by swiss param team that the ligand parameters generated by >>> swissparam could also be used with opls FF in principle as they are based on >>> MMFF >>> So, in order to cross check or validate my results i was trying to use >>> mktop to generate the ligand topologies for MD simulations. >>> >>> >> Maybe the SwissParam-generated topology will work. There are >> commonalities underlying these force fields, to be sure. Still, the >> methodology for properly deriving OPLS parameters is quite well described in >> the literature, right down to the QM basis sets required to run the geometry >> optimizations and charge calculations. >> >> -Justin >> >> Please let me know your comments and suggestions on the procedure , >>> regarding the compatibility of MMFF generated topologies to be used by OPLS >>> and other methods to validate my results. >>> >>> Thanks, >>> >>> Pramod >>> >>> On Wed, Oct 12, 2011 at 1:28 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >>> jalem...@vt.edu>> wrote: >>> >>> >>> >>> ram bio wrote: >>> >>> Dear Justin, >>> >>> Thanks for the information. >>> >>> Initially, i just wanted to run a simulation of protein-ligand >>> in water solvent . I renamed the topology.top generated from >>> mktop to ligand.itp; and included the ligand.itp line in the >>> topol.top file generated from the pdb2gmx. During the pdb2gmx >>> command, i used opls FF. The coordinates of ligand used as >>> input for mktop were added to the output of pdb2gmx (process.pdb >>> - only protein coordinates), so that the structure file along >>> with ligand coordinates (processlig.pdb) can be used for further >>> steps. I doubt whether the procedure followed by me is correct, >>> as when i execute grompp command to add ions i am getting errors : >>> >>> >>> grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr >>> >>> >>> ERROR 1 [file ligand.itp, line 291]: >>> No default Ryckaert-Bell. types >>> >>> .......... >>> >>> ------------------------------**__------------------------- >>> >>> Program grompp, VERSION 4.5.4 >>> Source code file: toppush.c, line: 1526 >>> >>> Fatal error: >>> [ file ligand.itp, line 397 ]: >>> Atom index (0) in dihedrals out of bounds (1-53). >>> This probably means that you have inserted topology section >>> "dihedrals" >>> in a part belonging to a different molecule than you intended to. >>> In that case move the "dihedrals" section to the right molecule. >>> For more information and tips for troubleshooting, please check >>> the GROMACS >>> website at >>> http://www.gromacs.org/__**Documentation/Errors<http://www.gromacs.org/__Documentation/Errors> >>> >>> <http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> >>> > >>> ------------------------------**__------------------------- >>> >>> >>> The commands executed to reach the grompp step are as follows: >>> >>> >>> pdb2gmx -f jhcdyinteractionposea.pdb -ignh -o process.pdb >>> editconf -f processlig.pdb -o procent.pdb -princ >>> editconf -f procent.pdb -o procent.gro -c -d 1.0 -bt cubic >>> genbox -cp procent.gro -cs spc216.gro -o procentsolv.gro -p >>> topol.top >>> grompp -f ions.mdp -c procentsolv.gro -p topol.top -o ions.tpr >>> >>> I have attached the topol.top, ligand.itp and procentsolv.gro >>> files for your information, Please let me know your suggestions >>> to fix this error. >>> >>> >>> The ligand.itp file is trash. Most of your atoms have zero charge >>> (except for a few that have +/- 1...yikes!) and on line 397 (as >>> cited in the error message) atom 0 is referenced, which of course >>> does not exist, since numbering starts with 1. You also have some >>> exotic atom types present, and thus bonded parameters cannot be >>> assigned, as grompp complained earlier. >>> >>> You need a better quality topology, and perhaps a different force >>> field that might be suited for doing these simulations. >>> >>> -Justin >>> >>> Thanks, >>> Pramod >>> >>> >>> >>> >>> >>> On Wed, Oct 12, 2011 at 12:38 PM, Justin A. Lemkul >>> <jalem...@vt.edu <mailto:jalem...@vt.edu> >>> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >>> >>> >>> >>> ram bio wrote: >>> >>> Dear Gromacs Users, >>> >>> I am using opls FF for my protein-ligand simulations in >>> lipid >>> bilayer. I have generated the topologies for the ligand >>> using >>> MKtop. The output from the MKTOP gives the top file, but >>> not the >>> coordinate/structure file. Please let me know if any >>> tutorial is >>> available for merging the output of mktop into gromacs MD >>> simulation. >>> >>> >>> >>> You can #include any molecule topology in a system .top, >>> provided >>> you have the right format: >>> >>> http://www.gromacs.org/____** >>> Documentation/File_Formats/.__**__itp_File<http://www.gromacs.org/____Documentation/File_Formats/.____itp_File> >>> <http://www.gromacs.org/__**Documentation/File_Formats/.__** >>> itp_File<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File> >>> > >>> >>> >>> <http://www.gromacs.org/__** >>> Documentation/File_Formats/.__**itp_File<http://www.gromacs.org/__Documentation/File_Formats/.__itp_File> >>> >>> <http://www.gromacs.org/**Documentation/File_Formats/.**itp_File<http://www.gromacs.org/Documentation/File_Formats/.itp_File> >>> >> >>> >>> There is no tutorial for using mktop with a >>> protein-ligand/membrane >>> system, but there are tutorials for protein-ligand complexes: >>> >>> http://www.bevanlab.biochem.__**__ >>> vt.edu/Pages/Personal/**justin/____gmx-tutorials/** >>> complex/index.____html<http://vt.edu/Pages/Personal/justin/____gmx-tutorials/complex/index.____html> >>> <http://vt.edu/Pages/Personal/**justin/__gmx-tutorials/** >>> complex/index.__html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html> >>> > >>> >>> >>> <http://www.bevanlab.biochem._**_ >>> vt.edu/Pages/Personal/justin/**__gmx-tutorials/complex/index.**__html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/complex/index.__html> >>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** >>> gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html> >>> >> >>> >>> and membrane protein systems: >>> >>> http://www.bevanlab.biochem.__**__ >>> vt.edu/Pages/Personal/**justin/____gmx-tutorials/** >>> membrane_____protein/index.**html<http://vt.edu/Pages/Personal/justin/____gmx-tutorials/membrane_____protein/index.html> >>> <http://vt.edu/Pages/Personal/**justin/__gmx-tutorials/** >>> membrane___protein/index.html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html> >>> > >>> >>> <http://www.bevanlab.biochem._**_ >>> vt.edu/Pages/Personal/justin/**__gmx-tutorials/membrane___** >>> protein/index.html<http://vt.edu/Pages/Personal/justin/__gmx-tutorials/membrane___protein/index.html> >>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** >>> gmx-tutorials/membrane_**protein/index.html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html> >>> >> >>> >>> -Justin >>> >>> -- ==============================**____========== >>> >>> >>> >>> 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> <http://vt.edu> | (540) >>> 231-9080 <tel:%28540%29%20231-9080> >>> <tel:%28540%29%20231-9080> >>> http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin >>> >>> <http://vt.edu/Pages/Personal/**justin<http://vt.edu/Pages/Personal/justin> >>> > >>> <http://www.bevanlab.biochem._**_vt.edu/Pages/Personal/justin >>> >>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>> >> >>> >>> ==============================**____========== >>> >>> >>> -- 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<http://lists.gromacs.org/____mailman/listinfo/gmx-users> >>> >>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >>> > >>> >>> >>> >>> <http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >>> >>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> >> >>> Please search the archive at >>> >>> http://www.gromacs.org/____**Support/Mailing_Lists/Search<http://www.gromacs.org/____Support/Mailing_Lists/Search> >>> >>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >>> > >>> >>> >>> >>> <http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >>> >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> > >>> <mailto:gmx-users-request@__gr**omacs.org <http://gromacs.org> >>> >>> >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> >>. >>> Can't post? Read >>> >>> http://www.gromacs.org/____**Support/Mailing_Lists<http://www.gromacs.org/____Support/Mailing_Lists> >>> >>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> > >>> >>> >>> <http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> >> >>> >>> >>> >>> -- ==============================**__========== >>> >>> 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 >>> <tel:%28540%29%20231-9080> >>> >>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >>> >>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >>> >>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> Please search the archive at >>> >>> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >>> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >>> >. >>> Can't post? Read >>> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >>> >>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> >>> >> -- >> ==============================**========== >> >> 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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