Hi, I edit my topology file for mutating CH --> COH during free energy calculation.
Since one hydrogen atom attached to carbon disappears, while two O and H atoms are appearing, I build topology file as follows: 8 opls_169 1 TEST O 3 -0.7 15.9994 opls_140 0.1 1.008 13 opls_140 1 TEST H6 4 0.1 1.008 opls_169 -0.7 15.9994 18 opls_155 1 TEST H10 5 0.455 1.008 DUM_155 0.0 1.008 25 DUM_155 1 TEST H15 7 0.000 1.008 opls_155 0.455 1.008 My questions are, 1. as you can see, I introduce a dummy atom in the A state and mutate H --> O and dummy --> H. Is it correct? 2. if it is correct, then how should I build bonded parameters between H (opls_140) and dummy (opls_155), since they do not exist. I have searched for mailing list and tutorials, but I am still not clear what is the correct way to edit topology file for my case. I will appreciate that if you can suggest or help me regarding this issue. Thanks. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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