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.
