Hello!
There are no parameters for copper atom (or any transition metal) in
the AMBER force fields. You have to load an external file with the
parameters for CU using the tleap command:
loadamberparams copper.frcmod
And in the copper.frcmod file something like:
-----------------------------------------------------------------------------------------------------------------------
MASS
CU 63.55
BOND
nb-CU 75.582 2.027
o-CU 84.879 1.907
ANGLE
ha-ca-nb 52.970 116.000 same as ha-ca-n2
ca-nb-CU 50.523 114.913 from g09 calculations
DIHE
ca-nb-cp-ca 1 4.800 180.000 2.000
ca-nb-cp-cp 1 4.800 180.000 2.000
nb-CU-nb-cp 1 14.800 180.000 2.000
IMPROPER
o- o-CU-nb 1.1 180.0 2.0
NONBON
CU 1.0330 0.0427 LJ parms from
http://dx.doi.org/10.1021/jp054177x
-----------------------------------------------------------------------------------------------------------------------
This is an example of a file to add parameters for a molecule with
copper that I am working on. Do not use for your particular system!
You have to generate the parameters for your specific system and test
it with short MD runs to see if the geometry of the complex is
correct.
Hope that helps a little!
Rodrigo.
On Mon, Jun 3, 2013 at 5:40 AM, Fabian Glaser <fglaser.technion.ac.il> wrote:
> Hi,
>
> I am trying to prepare a protein for MD with amber, using for example Maestro or Chimera. This protein has a Cu+2 atom. Once I have the partial charges and hydrogens, I save the molecule in mol2 format but when I open them with tleap for solvation, etc. it seems that the mol2 file is not read properly so the atoms are not properly recognized.
>
> For example:
> (using default radius 1.500000 for CD1)
> (using default radius 1.500000 for CD2)
> (using default radius 1.500000 for CE1)
> (using default radius 1.500000 for CE2)
>
> (using default radius 1.500000 for OH)
> (using default radius 1.500000 for CU)
>
> I have also tried the opposite reading pdb directly, but in this case the copper atom is not recognized:
>
> Unknown residue: CU number: 283 type: Terminal/last
>
> And then the charge is not correct.
>
> What is the right way to go?
>
> Thanks a lot,
>
> Fabian
> _______________________________
> Fabian Glaser, PhD
> Bioinformatics Knowledge Unit,
> The Lorry I. Lokey Interdisciplinary
> Center for Life Sciences and Engineering
>
> Technion - Israel Institute of Technology
> Haifa 32000, ISRAEL
> fglaser.technion.ac.il
> Tel: +972 4 8293701
> Fax: +972 4 8225153
>
>
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Received on Mon Jun 03 2013 - 08:00:02 PDT
