Dear Philippe,
we are following approach which is explained in this article:
ARMIN W. OPITZ, NORMAN J. WAGNER, Journal of Polymer Science: Part B:
Polymer Physics, Vol. 44, 3062–3077 (2006) VC 2006 Wiley Periodicals, Inc.
So yes for the parametrisation of the relevant residuies we are using
Antechamber, GAFF
(without relacing it by amber99). Regarding to atomtypes we are using that
which are generated by
Antechamber. In case that we are using atoms which are not still
parametrised within the Amber ff, we derive the relevant
parameters from QM calc and implement them in Amber using FRCMOD files.
Regarding to 10-12 hbonds interaction, we are using default compilation
setting where "DHAS_10_12" is not use
(see the amber manual for details) so we are not computing hbond
energetical interactions as the separate
contributions.
Best wishes,
Marek
Dne Thu, 16 Sep 2010 17:53:06 +0200 Philippe Pinard <pp_amber17.yahoo.com>
napsal/-a:
> Dear Dr Maly
>
> I found some of your emails on the amber archive about parameterization
> of
> dendrimers.
> Is it possible to mention what are the types you assigned to your G4
> atoms, did
> you use antechamber with GAFF, then replaced by hand the types to
> leap99? what
> types did you choose for the central residu, the building block spcer
> and the
> terminal i.e peripheral residus? I could not find any details elsewhere.
> Also did you use 10-12 hbond terms, is there a paper where you give
> details on
> these issues?
> Many thanks in advance
>
> regards
> P Pinard
>
>
>
> ________________________________
> From: Marek Maly <marek.maly.ujep.cz>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Tue, September 14, 2010 10:09:54 PM
> Subject: Re: [AMBER] list of atoms with associated total forces ?
>
> Dear Ben,
>
> thanks a lot for your valuable info !
>
> Best,
>
> Marek
>
> Dne Tue, 14 Sep 2010 22:45:39 +0200 Ben Roberts <roberts.qtp.ufl.edu>
> napsal/-a:
>
>> Hi Marek,
>>
>> On 14/9/2010, at 11:32 a.m., Marek Maly wrote:
>>
>>> Dear all,
>>>
>>> is there any way how to obtain, for the given frame from amber MD
>>> trajectory, list of chosen atoms with associated
>>> total forces acting on each atom in the given list ? If yes, is it also
>>> eventually possible to obtain more detail list
>>> where is listed nonbond and bond part of the total force acting on each
>>> atom ?
>>
>> You may want to check out the debug options. One in particular is the
>> "dumpfrc" option, part of the &debugf namelist, which will print the
>> total force on each atom, spitting it out to a file called
>> "forcedump.dat".
>>
>> As for how to get a breakdown of the forces by component, dumpfrc
>> provides some of this information, though it's not comprehensive. It
>> includes, I think, bond, angle and torsion forces. You could get other
>> components of the force indirectly, for example by running the same
>> calculation with and without the "zerochg" and "zerovdw" debugging
>> options and calculating the difference.
>>
>> HTH,
>>
>> Ben
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>>
>
>
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