Hi Thomas,
thanks for the feedback. I actually was quite curious about it.
Best regards
Alessandro
Il 21/05/2014 10:15, Thomas Exner ha scritto:
> 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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>> 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 Wed May 21 2014 - 01:30:03 PDT
