Dear Dr.Justin<br><br>I have read this section before.<br>There are 2 problem:<br>1:ADDHYD atomname and DELHYD atomname commands dosen't work!<br>they result in ERROR in PRODRG<br><br>2:Actually I don't know the additional hydrogen is necessary or not!<br>
Because it may be necessary for proper protonation.<br>My drug(Sertraline) is in a solvent,it may interact with water molecules and Nitrogen may get an additional hydrogen.<br><br>What do you think?<br><br><br><div class="gmail_quote">
On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation.<br>
<br>
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... ;)<br>
<br>
-Justin<div><div></div><div class="h5"><br>
<br>
TJ Mustard wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Yes I would recommend acpype.<br>
<br>
On February 9, 2011 at 9:42 AM <a href="mailto:jorge_quintero@ciencias.uis.edu.co" target="_blank">jorge_quintero@ciencias.uis.edu.co</a> wrote:<br>
<br>
> I think that is better to use antechamber tools.<br>
><br>
><br>
> > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:<br>
> >> Dear Users<br>
> >><br>
> >> I am using PRODRG to make topology for my drug<br>
> >> It addes Hydrogenes but in wrong way.<br>
> >> My Nitrogen atom is bonded to 2 Carbos,<br>
> >> and PRODRG addes 2 Hydrogenes to it .<br>
> >> Please let me know how can I do.<br>
> >> Thanks in advance<br>
> ><br>
> > This is not really the forum to get help about that. You need to read<br>
> > how to PRODRG needs input, and supply something it can deal with. Then<br>
> > do a whole bunch more work testing what it produced.<br>
> ><br>
> > Mark<br>
> > --<br>
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> Jorge R. Quintero<br>
> Químico<br>
> Universidad Industrial de Santander<br>
> Bucaramanga, Santander - Colombia<br>
><br>
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<br>
TJ Mustard<br>
Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a><br>
<br>
</blockquote>
<br></div></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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