Hello:
Beg pardon for the intrusion. Suppose you have modeled with DTF a
tetrahedral complex of Zn(II), two aspartates, one HIS, and one H2O. The
tetrahedral geometry is nearly perfect as it comes out from LEaP. However,
on MD, Zn(II) and the three CA/O/O of the aas lie on a plane, with apical
H2O. What would you conclude?
The DFT calculations were fine under every respect and the "bond" commands
with LEaP were appropriate. Looking at the distorted geometry with VMD, the
bonds created with the "bond" commad are not seen, while the interatomic
distances are correct for the required bonds, even after long MD
simulation. I am not familiar enough with prm/crd to check there for bonds
(which is an easy affair - for me - with psf)
Thanks for advice
francesco pietra
On Mon, Jun 3, 2013 at 4:51 PM, ros <rodrigogalindo.gmail.com> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 03 2013 - 08:30:02 PDT
