[gmx-users] PRODRG

[mohsen ramezanpour]

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

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.

What do you think?


On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul <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 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
>>  >
>>  > --
>>  > gmx-users mailing list    gmx-users at gromacs.org
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>>
>>
>> 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
>
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