mohsen ramezanpour wrote:
Dear Dr.Justin
I did it,it works.Thanks.
there are another problem:
I want to add some hydogens to my topology.
I used ADDHYD atomname,But this dosen't work.
PLease let me know how can I include some Hydrogenes in my topology.
Use a different force field and don't use PRODRG. Gromos96 is a united-atom
force field.
-Justin
Thanks in advance
Mohsen
On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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_quint...@ciencias.uis.edu.co
<mailto:jorge_quint...@ciencias.uis.edu.co>
<mailto:jorge_quint...@ciencias.uis.edu.co
<mailto: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
> > --
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> --
> Jorge R. Quintero
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> Universidad Industrial de Santander
> Bucaramanga, Santander - Colombia
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Email: musta...@onid.orst.edu
<mailto:musta...@onid.orst.edu> <mailto:musta...@onid.orst.edu
<mailto:musta...@onid.orst.edu>>
-- ========================================
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Ph.D. Candidate
ICTAS Doctoral Scholar
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Virginia Tech
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Virginia Tech
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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
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