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
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Received on Wed Sep 21 2011 - 08:30:03 PDT
