Hi!,
Please find leaprc, lib and frcmod files with examples to Zn+2 proteins in
the link:
http://mayoresearch.mayo.edu/mayo/research/camdl/zinc_protein.cfm
Regards,
Hector.
On Thu, 22 Sep 2011, Bruno Luís Pinto de Oliveira wrote:
> Dear Zhu
look at this paper...
http://pubs.acs.org/doi/abs/10.1021/ct1002626
it can be usefull to you...
Regards, BL
Dear Kk Zhu，
> Thanks for your advice! But i still have some questions for your
> help. At first, i want to make the zinc atom bond to the HIS through
> the ZN--NB,and make the HIS a nonstandard residue,but i cannot find
> the point charge for the residue.
If nobody studied your complex before you, you should derive the
charges for this complex (atomic charges are generally not
transferable between molecules/complexes).
> I know the R.E.D. Server that you mentioned could solve the problem
> ,is that right ?
R.E.D. and R.E.D. Server derive RESP or ESP charges embedded in force
field library(ies) for new molecules and new molecular fragments.
> i also tried to use the R.E.D. Server but it is very hard for me a beginner.
In your case, there are two main difficulties:
- deriving RESP or ESP charges embedded in force field library(ies)
for new molecules and new molecular fragments
- working on a bio-inorganic complex
> If there are other method except this?
You need to demonstrate that your complex is valid; QM is an efficient
method to study organic and bio-inorganic molecules.
> The second question is if i bond the zinc to the residues around it
> where can i find the parameters ,for example the angles and the
> dihedrals ?
- You first derive charges for your complex
- Then, you need to define the FF atom types; here, because of the
symmetry of the complex two atoms having a similar chemical
environment might have different FF atom types.
- van der Waals parameters can be obtained from the literature
- Equilibrium values for bonds and angles can be obtained from X-ray
data (or from QM)
- bond and angle FF constants can be obtained from literature or from
fitting from QM data
- dihedral FF parameters (energy barrier) involving the metal centre
are often set to zero
> I also want to know i deal with my system llke this is right or wrong !
I do not understand what you mean.
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
--
---------------------------------------
Dr. Hector A. Baldoni
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917
5700 San Luis - Argentina
hbaldoni.unsl.edu.ar
---------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 22 2011 - 07:30:03 PDT
