I know that should not make the difference, but you might try to assign
amber ATs (N3 and H, assuming you are using a amber ff). N3 (as well as
n4...) should remain tetrahedral even in higly polar environments, so I
guess that the problem is in the prep/mol2/off (you might also try to
change the format of the NH4+ parameter file. This is again useful only
for debugging, as different formats should give the same result...)
Best.
Alessandro
Il 19/05/2014 15:00, Thomas Exner ha scritto:
> 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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
ResearcherID: F-5064-2012
URL: http://www.researcherid.com/rid/F-5064-2012
skype alessandrocontini
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Received on Mon May 19 2014 - 07:00:02 PDT
