[gmx-users] PRODRG

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear Dr.Justin
> 
> I have read this section before.
> There are 2 problem:
> 1:ADDHYD atomname and DELHYD atomname  commands dosen't work!
> they result in ERROR in PRODRG
> 

You have to run PRODRG twice.  The first time, you get the wrong output.  Note 
the atom name that PRODRG assigns to your N atom.  The second time, use DELHYD 
(name).  If that doesn't work, then I have no idea and you're better off 
submitting your question to the PRODRG developers.

> 2:Actually I don't know the additional hydrogen is necessary or not!
> Because it may be necessary for proper protonation.
> My drug(Sertraline) is in a solvent,it may interact with water molecules 
> and Nitrogen may  get an additional hydrogen.
> 

A doubly-protonated secondary amine would be a fairly strong acid.  You should 
do a pKa calculation to determine what is relevant rather than guessing.  There 
are web servers and other software out there that can do this for you.  Google 
is your friend.

-Justin

> What do you think?
> 
> 
> On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
>     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
>         <mailto: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
>          > > --
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>          >
>          >
>          > --
>          > Jorge R. Quintero
>          > Químico
>          > Universidad Industrial de Santander
>          > Bucaramanga, Santander - Colombia
>          >
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> 
>          
>         TJ Mustard
>         Email: mustardt at onid.orst.edu <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

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

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