I'm completely in agreement with that advice. To use antechamber tool, I recommend use force field for all the system.
> > The OP's question is easily answered by referring to the PRODRG FAQ in > dealing > with proper protonation. > > As for Antechamber and the like, these are good tools, but do not produce > GROMOS-compatible topologies, if that is indeed the underlying goal. > We've done > thorough analysis of various QM calculation methods for GROMOS charges, > and none > of them produce completely satisfactory topologies. Antechamber, Spartan, > Gaussian, etc are good for initial charge calculations, but IMHO do not > qualify > as an "end result" for GROMOS parameterization due to the empirical > refinement > used in the force field derivation. All of that makes GROMOS > parameterization > somewhat tricky, and hence why force field choice is so incredibly > important > when designing projects... ;) > > -Justin > > TJ Mustard wrote: >> >> >> Yes I would recommend acpype. >> >> On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote: >> >> > I think that is better to use antechamber tools. >> > >> > >> > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: >> > >> Dear Users >> > >> >> > >> I am using PRODRG to make topology for my drug >> > >> It addes Hydrogenes but in wrong way. >> > >> My Nitrogen atom is bonded to 2 Carbos, >> > >> and PRODRG addes 2 Hydrogenes to it . >> > >> Please let me know how can I do. >> > >> Thanks in advance >> > > >> > > This is not really the forum to get help about that. You need to >> read >> > > how to PRODRG needs input, and supply something it can deal with. >> Then >> > > do a whole bunch more work testing what it produced. >> > > >> > > Mark >> > > -- >> > > 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 >> > > >> > >> > >> > -- >> > Jorge R. Quintero >> > QuÃmico >> > Universidad Industrial de Santander >> > Bucaramanga, Santander - Colombia >> > >> > -- >> > 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 >> > >> >> >> >> TJ Mustard >> Email: musta...@onid.orst.edu >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- 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