[gmx-users] PRODRG

[Justin A. Lemkul]

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_quintero at 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 at 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-request at 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 at 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-request at gromacs.org.
>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  >
> 
>  
> 
> TJ Mustard
> Email: mustardt at 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

========================================