[AMBER] About geometry of FAD in the F-90 project of http://q4md-forcefieldtools.org/

From: Emilio Lence <guitarro.de.meixente.gmail.com>
Date: Fri, 31 Oct 2014 13:47:31 +0100

Dear all.
Recently I started working with a protein that has FAD and NADP as
cofactors. Searching y found that the http://q4md-forcefieldtools.org/ has
a project call F-90 which includes a lot of cofactors. After a few problems
I finally set everything correctly for my simulation.
But when checking the mol2 files of the FAD and NADP1 I realised that the
geometry in the FAD is wrong. When looking at the part with the 3 fused
six-member rings, in the central ring there is a bond between the N and one
of the carbon atoms with a distance of 0.78 A, that is obviously wrong. I
checked then the topology and coordinates files generated, and they have
the same bond distance.
So, my question is if anyone that has performed MD simulations with this
parameters, and if this simulations have shown any troubles or extrange
behaviours of the FAD cofactor?
Thanks for your kind attention.
Cheers, Emilio.
AMBER mailing list
Received on Fri Oct 31 2014 - 06:00:05 PDT
Custom Search