Hi Mohsen, Now I wouldn't want to get in the way of excellent ideas :) Check the PRODRG FAQ. It is explained there (somewhere) how to force inclusion of hydrogens.
Cheers, Tsjerk On Feb 6, 2011 11:39 AM, "mohsen ramezanpour" <[email protected]> wrote: Dear Dr.Tsjerk I know it.I know PRODRG is not very valid for evaluating free energies(According to Dr.Justin article) too. But the problem is here: If I know all of hydrigenes are polar,how can I have a topology with all of them? Actually there are so many polar H in my small molecules which are not included in topology file!! These can change the number of Hydrogen bonds and as a resut my binding free energy!!! I want to do a new work about these,I have something excellent in my mind. I only need a topology file with all hydrogenes in 43A1 force field. Is there any way(except manually adding hydrogenes)? Please let me know. I will present a new and excellent method instead of using PRODRG Thanks in advance Mohsen On Sun, Feb 6, 2011 at 1:23 PM, Tsjerk Wassenaar <[email protected]> wrote: > > Hi Mohsen, > > So ... -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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