[gmx-users] PRODRG
Justin A. Lemkul
jalemkul at vt.edu
Fri Feb 11 12:32:00 CET 2011
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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>
> <mailto: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> <mailto: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> <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 <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
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