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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- application/octet-stream attachment: HAL.mol2
Received on Mon Jul 04 2016 - 07:30:03 PDT
