Hallo Alessandro:
Thank you for your quick reply.
N = n4 and H = hn: So this looks fine to me.
Best.
Thomas
Alessandro Contini schrieb:
> Hi Thomas,
> what kind of AT has been assigned to N? I think the problem is there;
> check that N is assigned as N3 (amber AT, same as ammonium in Lys) or n4
> (gaff AT).
>
> Hope this help
>
> Alessandro
>
>
> Il 19/05/2014 14:31, Thomas Exner ha scritto:
>> Dear AMBER users:
>>
>> 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?
>>
>> Thank you very much.
>> Thomas
>>
>>
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>>
>
>
--
________________________________________________________________________________
PD 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 Mon May 19 2014 - 06:30:02 PDT
