Dear B. Sangeetha,
> I want to simulate a protein with HHCC zing finger motif along with Zinc in
> a bonded model (since the Zn2+ atom is structurally important).
> I have separated the motif along with zinc from the crystallographic
> structure and used this as starting geometry to generate ESP data using
> Gaussian03.
> While I try to generate RESP charges from this ESP, I face some problems.
> 1. How to cap the individual residues? If I use a CH3 cap, I will not be
> able to neutralize the net charge on each residue.
In general one caps each residue (ligands of the metal in your case)
by the ACE and NME capping groups; although other approaches are
always possible.
You only total charges to consider are:
- the total charge of the entire complex
- the total charge value of each capping group (equals zero)
You might consider the charge value of the Zinc atom (see below).
> 2. If I use ACE, NME caps, then I would have to define more than one group
> constraint (one group for each residue). But, RESP does not recognize the
> group constraints. The charges from 1st stage RESP fitting is similar with
> and without group constraints.
I am not sure I understand what you mean.
May be you could use the R.E.D. tools and/or R.E.D. Server at
http://q4md-forcefieldtools.org... Charge fitting and force field
library building are carried out from an input PDB file.
PDB ---> P2N ---> mol2 files
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
You could start by deriving RESP charges for a dipeptide molecule;
then for the central fragment of this dipeptide and finally for your
Zinc complex composed of several dipeptides...
See
http://q4md-forcefieldtools.org/Tutorial/
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#8
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#9
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
> 3. The net charge on all atoms, HHCC+Zn2+ is 0, whereas the charges on both
> cysteines should be -1. If I need to use a bonded approach, then how should
> i treat the Zn2+ atom?
You could let the charge fitting step calculate the charge value for
the Zinc atom without constraint _for this Zinc atom_, or force a +2
charge value for the Zinc atom using an intra-molecular charge
constraint...
See
http://q4md-forcefieldtools.org/REDDB/projects/F-88/ (iron complex)
http://q4md-forcefieldtools.org/REDDB/projects/F-89/
(ChemPlusChem in press)
> Whether it should be included as a part of one of
> the residues (as in advanced version of Tutorial A1)
(I do not think this tutorial "AMBER ADVANCED TUTORIALS/TUTORIAL A1"
is a reference.
This was discussed several times...)
> or treated separately
> with a charge of +2? If I include the Zn2+ atom as a part of any residue,
> then how can I maintain the -1 on cysteines?
Both approaches can be followed; then, you can decide to create bonds
(or not create) between the metal and the ligands.
See once again
http://q4md-forcefieldtools.org/REDDB/projects/F-88/
http://q4md-forcefieldtools.org/REDDB/projects/F-89/
(this is just an example of what can be done)
You can find ESP and RESP inputs as well there...
http://q4md-forcefieldtools.org/REDDB/projects/F-88/input1.in
http://q4md-forcefieldtools.org/REDDB/projects/F-89/input1.in
http://q4md-forcefieldtools.org/REDDB/projects/F-89/input2.in
> I am using Amber 11 (bugfix upto 17) with Amber Tools 1.5 (bugfix upto 12).
> I have attached my input and output files for the 1st stage RESP fitting.
> Any advice in this regard would be very helpful.
This is difficult to help without the corresponding PDB file...
regards, Francois
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Received on Mon Sep 03 2012 - 12:00:03 PDT
