Quoting Jiayun Pang <Jiayun.Pang.manchester.ac.uk>:
> I am doing MDs using amber FF94 and amber 9 to an enzyme with a rather
> unusual substrate. Please see the attached pdb for the structure. I
> have added NME and ACE to cap the N-H and C=O termini.
This is an interesting ligand for a new charge derivation procedure.
> It has three TRP like residues that covalently bound to each other
> (named as TTW, TTR and TRR in pdb).
This means you could use TRP as a starting building block for your
whole ligand...
> My question is what's the best way to obtain the RESP charge for it? Is
> it necessary to treat them as one unit, calculate ESP charge in
> Gaussian, then fit the RESP using either antechamber or RED? I suppose,
> with a structure as big as this, the final RESP charge will be quite
> conformation-dependent.
I agree.
> Alternatively, to reduce the complexity, I could omit TRR and use the
> charge of standard TRP residue for it. But how should I adjust the
> charge of CG, CD1, NE1 to accommodate the loss of the H connected to
> CD1.
>
> Another thing is, TTR is exactly like the sidechain of TRP. Could I
> apply similar charges of TRP for it as well?
You could compute new charges for your ligand:
1- Select the conformations (phi, psi & chi...) of ACE-TRP*-NME (TRP*
being your modified TRP)
For that, you could follow what has been done for the 'natural' TRP as in
Cieplak et al. J. Comput. Chem., 1995, 16, 1357-1377
2- Find the linking group(s) allowing the connections between two TRP*
The key ;-)
3- Use the INTER-MCC keyword in R.E.D. to define your new fragments such as:
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11
TABLE 17
Here, you could also use the INTER-MEQ keyword, to force charge
values of identical atoms in different TRP* to be equivalent
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11
TABLE 18
4- Associate your different TRP* fragments using a LEaP script.
regards, Francois
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Received on Wed May 21 2008 - 06:07:18 PDT
