Hello Users, I was trying to run grompp for a membrane protein - ligand dynamics. I am using 4 5 ligands together. Under grompp run I got error overriding atomtype HGP1. Came out two ligands were sharing similar naming in atomtype section. I wanted to ask is it harmless to change it manually are there any conventions for it ? following this are there any other changes in topology file that i need to make? [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 CG2O6 6 12.0110 0.600 A 3.56359487256e-01 2.928800e-01 HGP1 1 1.0080 0.340 A 4.00013524445e-02 1.924640e-01 NG2S2 7 14.0070 -0.690 A 3.29632525712e-01 8.368000e-01 OG2D1 8 15.9994 -0.580 A 3.02905564168e-01 5.020800e-01 ; [ atomtypes ] ; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14 HGP1 1 1.0080 0.500 A 4.00013524445e-02 1.924640e-01 OG311 8 15.9994 -0.500 A 3.14487247504e-01 8.037464e-01 * thank you for your precious time.*
* with regards* *Yogesh Sharma* -- 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.