On 3/19/18 10:05 AM, Upendra N wrote:
Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp and cordinates) <http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2anton.py> then I included ligand.itp to the main topology file and appended the ligand coordinates to the protein coordinates to make the protein-ligand structure coordinate file. Further steps such as editconf and genbox went smoothly. But In the grompp step, I get an error as follows, *ERROR 13 [file gd2.itp, line 248]: No default U-B typesERROR 14 [file gd2.itp, line 258]: No default U-B types......................ERROR 23 [file gd2.itp, line 371]: No default Improper Dih. types* .... Kindly help to fix this error. I also tried to defining with define = -DUSE_OLD_C36 and inculded #ifdef USE_OLD_C36 #include "old_c36_cmap.itp" in *.top #endif again obtained the same error. Please help me out here.
Don't use old parameters unless you specifically need them. C36m is an improvement over C36.
Your problem is probably that the script produced a .prm file with additional parameters needed by your ligand. You need to #include this in your topology.
-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.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.
