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>> 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> 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
> > --
> > gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
> --
> Jorge R. Quintero
> Químico
> Universidad Industrial de Santander
> Bucaramanga, Santander - Colombia
>
> --
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
TJ Mustard
Email: musta...@onid.orst.edu <mailto:musta...@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> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
