Hi Diane Thanks for writing in. I guess I should have mentioned this earlier. To obtain partial charges for my substrate topology, I do an abinitio calculation (B-3LYP/6-31G*) and get the Chelpg and MKS charge distributions using Gaussian. Then I try and fit these charges to the steroid based on (1) previously defined GROMOS topologies (2) The charge group formulation.
I am fairly confident of my selection of atom types, bond types and bond angles. To be honest I did these parts on my own. The selection of improper and proper dihedrals remains a primary concern for me. It is primarily for this that I used the PRODRG server. I generally do a steepest descenet energy minimization followed by 5 ps of MD (with gradually reduced restrainsts), and I repeat this for about 100ps to equilibrate the protein. It is when I take off all restraints and run the final MD (after energy minimization without restraints) that i see weird artifacts coming in. I have tried different topologies with varying dihedrals and have seen weird things. I will really appreciate it if you could provide me with a topology you have previously used for a steroid, especially the section on proper and improper dihedrals. With regards Dhruv __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
