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On 11/02/2011 8:18 PM, mohsen ramezanpour wrote:
<blockquote
cite="mid:AANLkTikgvakUo2Onxpb2kzrxECCHzVrenb1MJ6+JjzHh@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
As Justin suggested, this is not the right forum for PRODRG advice.
This forum is for GROMACS discussions. I can only suggest you read
the PRODRG documentation.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTikgvakUo2Onxpb2kzrxECCHzVrenb1MJ6+JjzHh@mail.gmail.com"
type="cite">
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 moz-do-not-send="true"
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
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a> <mailto:<a
moz-do-not-send="true" 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 moz-do-not-send="true"
href="mailto:jorge_quintero@ciencias.uis.edu.co"
target="_blank">jorge_quintero@ciencias.uis.edu.co</a><br>
</div>
<div class="im"> <mailto:<a moz-do-not-send="true"
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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href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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<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>
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<br>
-- <br>
<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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