Dr Spoel, Thanks for your suggestions. Actually i would be using the GROMOS96 force field(option 0 in pdb2gmx GROMOS96 43a1).I am new to the GROMACS package.I wish to simulate a ligand-protein system and had been using the drug-enzyme tutorial available for this purpose. In the tutorial they use the PRODRG2 server to generate the ligand structure files. I find that the charges were calculated for a structure with only polar hydrogens present. This is then used to form the ligand-protein complex and solvation, neutralization etc.I was wondering
1) which ligand file should i use to generate my gaussian inputs. one with all the hydrogens or one with just the polar hydrogens. 2) I presume that for the gaussian calculation I have to submit an all hydrogen structure. In that case how do I refit the charges onto the polar hydrogen only structure which i will use for the generataion of the ligand-protein complex(as per the tutorial) 3) Do you think that the current forcefield is good for simulation of ligand-protein complexes. Kindly help me with your suggestions.Thanks so much Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 _______________________________________________ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
