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 <tsje...@gmail.com> wrote: > Hi Mohsen, > > So you want to have a topology with all atoms for use in a united atom > force field? Seems a bit awkward... PRODRG will only include polar > hydrogens, in accordance with the GROMOS force field. It won't be a > particular trustworthy topology, though, but you've probably caught the > words of caution expressed regularly on this list. > > Cheers, > > Tsjerk > > On Feb 6, 2011 9:42 AM, "mohsen ramezanpour" <ramezanpour.moh...@gmail.com> > wrote: > > Dear All > > I want to generate a topology file in 43A1 force field for a small > molecule. > Of course I want one which contains all hydrogens in that. > PRODRG doesn't generate like this.do you know another server with these > conditions? > > Thanks in advance > Mohsen > > -- > 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 > > > -- > 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 >
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