Re: [AMBER] nonbond parameter for copper(Ⅱ) ion

From: Marek Maly <>
Date: Sat, 16 Jul 2011 23:47:54 +0200


I am also interested about Cu++ Vdw parameters compatible with Amber ff.

I already checked source suggested by Rodrigo ("T Hermann and H Heumann,
RNA 1995 1: 1009-1017")
and I unfortunately didn't find any sentence about how they derived these
Moreover I also noticed that they used parameters for Mg++ r_Vdw = 1.17 A
and epsilon = 0.1 kcal/mol
claiming here that these data are from Aqvist JPC 1990,94,8021 although
after my recalculation of Mg++
parameters from this work I have obtained r_Vdw = cca 0.923 A and epsilon
= cca 0.875 kcal/mol (see attached file). Values
 from parm99.dat are r_Vdw = 0.7926 A and epsilon = 0.8947 kcal/mol. In
parm99.dat there is notice
(Mg2+ Aqvist JPC 1990,94,8021.(adapted)) which is obvious here but in case
of "T Hermann and H Heumann, RNA 1995 1: 1009-1017"
there is almost 9 x smaller well depth (epsilon) than in case of Aqvist.
This of course may put some doubts also
to reported Cu++ parameters especially if they do not clearly explain how
they derived them or from which another
work they adopted them (so that one could check in the original work that
data was adopted in the right way).

I attached my transformation of AI and BI Vdw parameters into Amber parm
format r_vdw and epsilon (well depth).

Any comments welcomed !

   Best wishes,


Dne Sat, 16 Jul 2011 03:58:06 +0200 ros <>

> Hello!
> You can use the parameters used by Hermann, T and Heumann, H. RNA,
> 1995, 1, 1009-1017
> r_{vdW}=0.96
> \epsilon=0.01
> I used those parameters for copper complexes and work acording to
> X-ray observations. Remember to check you simulated copper structure
> with some experimental data.
> Good luck!
> Rodrigo.
> 2011/7/15, caobb0214 <>:
>> Dear Sir,
>> There is a Cu2+in my molecule and I need its nonbond parameter (van der
>> Waals radius and well depth) in amber 9. can anyone help
>> _______________________________________________
>> AMBER mailing list

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Received on Sat Jul 16 2011 - 15:30:03 PDT
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