Dear Dr.Justin<br><br>I did it,it works.Thanks.<br><br>there are another problem:<br>I want to add some hydogens to my topology.<br>I used ADDHYD atomname,But this dosen't work.<br>PLease let me know how can I include some Hydrogenes in my topology.<br>
Thanks in advance<br>Mohsen<br><br><div class="gmail_quote">On Thu, Feb 10, 2011 at 7:56 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;">
<div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote>
<br></div>
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.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
What do you think?<div class="im"><br>
<br>
<br>
On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
The OP's question is easily answered by referring to the PRODRG FAQ<br>
in dealing with proper protonation.<br>
<br>
As for Antechamber and the like, these are good tools, but do not<br>
produce GROMOS-compatible topologies, if that is indeed the<br>
underlying goal. We've done thorough analysis of various QM<br>
calculation methods for GROMOS charges, and none of them produce<br>
completely satisfactory topologies. Antechamber, Spartan, Gaussian,<br>
etc are good for initial charge calculations, but IMHO do not<br>
qualify as an "end result" for GROMOS parameterization due to the<br>
empirical refinement used in the force field derivation. All of<br>
that makes GROMOS parameterization somewhat tricky, and hence why<br>
force field choice is so incredibly important when designing<br>
projects... ;)<br>
<br>
-Justin<br>
<br>
<br>
TJ Mustard wrote:<br>
<br>
<br>
<br>
Yes I would recommend acpype.<br>
<br>
On February 9, 2011 at 9:42 AM<br>
<a href="mailto:jorge_quintero@ciencias.uis.edu.co" target="_blank">jorge_quintero@ciencias.uis.edu.co</a><br></div><div class="im">
<mailto:<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<br>
need to read<br>
> > how to PRODRG needs input, and supply something it can deal<br>
with. Then<br>
> > do a whole bunch more work testing what it produced.<br>
> ><br>
> > Mark<br>
> > --<br>
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Email: <a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a> <mailto:<a href="mailto:mustardt@onid.orst.edu" target="_blank">mustardt@onid.orst.edu</a>><div class="im"><br>
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<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></div>
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-- <br><div><div></div><div class="h5">
========================================<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>
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