This is certainly a reasonable question for the AMBER list, but if you ask
the GLYCAM list, you will get more responses because most of our group
monitors it. That list is also archived publicly.
https://listserv.uga.edu/cgi-bin/wa?A0=GLYCAM-L
On Mon, Jul 4, 2016 at 10:03 AM, Casalini Tommaso <
tommaso.casalini.chem.ethz.ch> wrote:
> Dear Amber users and developers,
> I need to compute atomic charges for a modified glucuronic acid units, to
> be used with GLYCAM force field.
> According to literature, the procedure should be the following (very
> briefly):
>
>
> 1) Calculation of a first set of atomic charges at HF/6-31* level of
> theory through RESP;
>
> 2) 50 ns MD simulation in explicit solvent of the methyl-capped
> single unit;
>
> 3) Calculation of ensemble-averaged charges over 100-200 structures
> taken from MD simulations at HF/6-31G* level of theory (after optimization
> at same level of theory restraining exocyclic bonds) through RESP with qwt
> = 0.01. Aliphatic hydrogen charge is set equal to zero.
>
> I followed the approach that I have briefly summarized.
> I attach a mol2 file of my non-terminal unit. I am not convinced by the
> charges, since nitrogen charge is quite high. I checked other units
> available in GLYCAM library and nitrogen atoms are much more negative.
> Adopting a qwt = 0.001 charges seem more reasonable to me, but this would
> be not consistent with the official protocol of the force field.
> Have you some suggestions?
> I thank you in advance for your help.
> Best regards,
> Tommaso
>
> Tommaso Casalini, PhD
> Post Doctoral Fellow
> ETH Zurich
> Institute for Chemical- and Bioengineering
> Morbidelli Group, HCI F137
> Vladimir-Prelog-Weg 1
> 8093 Zurich, Switzerland
> tommaso.casalini.chem.ethz.ch<mailto:tommaso.casalini.chem.ethz.ch>
> Phone: +41 (0)44 632 61 83
>
>
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>
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Jul 04 2016 - 23:00:02 PDT
