Dear Francois and Alessandrro:
Thank you very much for your help. Francois: Your parameters work
perfectly! Special thanks to you!! The problem was the combination of
the partial charges assigned by RESP fitting and the very polar and
highly charged binding site. The protons were assign a charge of almost
1 and the nitrogen of -3. Thus, the protons and the nitrogen were pushed
to the negative and positive charged side chains, respectively. With a
small positive charge on the nitrogen and the protons in the new
parameter set this cannot happen anymore.
Best regards.
Thomas
FyD wrote:
> Dear Thomas,
>
>> At the moment I am fighting with a problem, which I expected to be
>> trivial. I would like to use an ammonium ion (NH4+) in a simulation of a
>> protein-ligand complex. To make things easy, I just used antechamber for
>> the parameterization. The resulting charges look pretty reasonable.
>> However, when minimizing the system, the ammonium ion gets completely
>> deformed with all protons on one side of the nitrogen atom in an almost
>> perfect square. The binding site is very polar and I am wondering if
>> this could be causing the problem.
>>
>> Is there any possible way to keep the tetrahedral conformation without
>> strongly constraining it?
>
> I generated a force field for NH4+ using R.E.D. Server Dev/PyRED at
> http://q4md-forcefieldtools.org/REDServer-Development/
>
> See the data for NH4+:
>
> http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFZJlwJvMK_Thomas-Exner/
>
> the force field library is at:
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFZJlwJvMK_Thomas-Exner/NH4+/Data-R.E.D.Server/Mol_m1/Mol-sm_m1-c1.mol2
>
> you go in 'NH4+/Data-R.E.D.Server/Data-Default-Proj'
> & you run leap:
> tleap -f leaprc.q4mdfft
>
> regards, Francois
>
>
>
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>
--
________________________________________________________________________________
Dr. Thomas E. Exner
Theoretische Pharmazeutische Chemie & Biophysik
Lehrstuhl Pharmazeutische Chemie
Pharmazeutisches Institut
Eberhard Karls Universität Tübingen
Auf der Morgenstelle 8 (Haus B)
72076 Tübingen
Germany
Tel.: +49-(0)7071-2976969
Mobil: +49-(0)171-3807485
Fax: +49-(0)7071-295637
E-Mail: Thomas.Exner[at]uni-tuebingen.de
Fachbereich Chemie und Zukunftskolleg
Universität Konstanz
78457 Konstanz
Germany
Tel.: +49-(0)7531-882015
Fax: +49-(0)7531-883587
E-Mail: Thomas.Exner[at]uni-konstanz.de
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Received on Wed May 21 2014 - 01:30:03 PDT
