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
****************
Il 5 x mille alla nostra Università è un investimento sui giovani,
sui loro migliori progetti.
Sostiene la libera ricerca.
Alimenta le loro speranze nel futuro.
Investi il tuo 5 x mille sui giovani.
Università degli Studi di Milano
codice fiscale 80012650158
http://www.unimi.it/13084.htm?utm_source=firmaMail&utm_medium=email&utm_content=linkFirmaEmail&utm_campaign=5xmille
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 19 2014 - 06:00:05 PDT
