From: luca belmonte (lucabelmonte_at_gmail.com)
Date: Fri Jun 24 2016 - 03:04:02 CDT
Ciao Francesca,
You may be interested in this work published on PCCP.
I used a custom version of the Charmm FF but I did not published results on
CuII and CuI.
At least you can get some informations on how to proceed, if you want to
reparameterize Cu interactions.
If you have any question, please send me an email.
Hope this helps,
Cheers,
http://pubs.rsc.org/en/content/articlelanding/2016/cp/c6cp00608f/unauth#!divAbstract
2016-06-24 9:19 GMT+02:00 Francesca Lønstad Bleken <
FrancescaL.Bleken_at_sintef.no>:
> Hi,
>
>
>
> I wish to do MD on a Cu containing Enzyme with NAMD and have a question on
>
> the treatment of the Cu and amino acids bound to the Cu as well as
>
> force field choice. Similar systems to ours have been used before and they
> have used
>
> GROMOS96 and OPLS2005 and kept bonds and angles to the
>
> Cu atoms fixated. I intend to do similarly, but am thinking about using
> CHARMM36 if possible.
>
> As far as I can see there are no CHARMM parameter for Cu(I) or (II).
>
> Are these available and usable with NAMD? If not, what forcefield do you
> suggest to use or have experience with on similar problems?
>
> I am also not entirely sure how to treat the amino acids
>
> connected to the Cu..
>
>
>
> I am aware that I will not be able to study chemistry of the part of the
> enzyme close to the Cu with this method
>
> (we do QM for that). With this I wish to look at the stability of the
> various parts of the enzyme (not close to Cu as these are fixed)
>
> over time.
>
>
>
> I am grateful for any help/directions/links/tutorials.
>
>
>
> Best regards,
>
> Francesca
>
>
>
>
>
-- Luca Belmonte, PhD CIBIO - Center for Integrative Biology University of Trento Phone: +39 0461 28 53 41 Mobile: +39 328 45 81 762
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