LigParGen generates new atom types for each ligand topology it generates. The output files from LigParGen should contain terms for opls800-925 (if necessary) in the generated topology file. These need to be included in the force-field file you use for use in your simulations.
A warning should be made about LigParGen: each atom is given a unique atomtype. For instance if you have a 25 atom ligand, you will have atomtypes opls 800 through opls824. Some of these may be repeats. This means that if you want to run with a different ligand you have to change these atomtype definitions each time. Hope that helps. =================== Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Wednesday, July 25, 2018 8:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization On 7/24/18 7:24 AM, farial tavakoli wrote: > Dear Justin > > I used LigParGen server to generate ligand topology but I dont know what > changes I have to do in .itp file. > when I issued this command: > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor > > faced this error:ERROR 1 [file LIG.itp, line 11]: > Atomtype opls_800 not found > I checked the aminoacids.rtp file of > /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not > atomtype opls_800 and 801 and ... in this file. while the LIG.itp which > generated by LigParGen server has atomtype opls_800 , 801 and ... . > I have to modify all of these atomtype opls_ in order to correspond to with > aminoacid.rtp file? > I would be thankfull if you help me. > bestFraial It looks like your topology introduces new atom types. Check the LigParGen documentation to see if it requires a different version of the force field or if the parameters are provided somewhere. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.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.