Dear Amber users,
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.
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.
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? Whether it should be included as a part of one of
the residues (as in advanced version of Tutorial A1) 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?
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.
--
Thank you,
With regards,
B. Sangeetha
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Received on Sun Sep 02 2012 - 06:30:02 PDT
