On Thu, Mar 22, 2012 at 10:42 PM, Gurunath Katagi <gurunath.katagi.gmail.com
> wrote:
> Dear all,
> i am trying to a do a simulation of a reduced cytochrome c protein [pdbid:
> 2GIW], using Amber forcefield (amber99sb) .
>
> using the RESP charges provided in the paper by Prof.Zaida Luthey-Schulten
> (http://onlinelibrary.wiley.com/doi/10.1002/jcc.20079/pdf), i have created
> the lib files for 2 cysteines (CYM), 1 histidines(HIC), 1 methionine(MEM)
> and HEM moeity and tried to prepare the frcmod and prepin files.
> but, i am getting the following error while creating the frcmod files for
> the molecule :
>
How did you create the lib files? I'm guessing these residues (CYM, HIC,
MEM) are all bonded to the heme group?
building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Could not find angle parameter: SH - CY - CB
> Could not find angle parameter: SH - CY - HC
> Could not find angle parameter: SH - CY - CX
> Could not find angle parameter: CT - SH - CY
> Could not find angle parameter: SH - CY - CB
> Could not find angle parameter: SH - CY - HC
> Could not find angle parameter: SH - CY - CX
> Could not find angle parameter: CT - SH - CY
> Could not find angle parameter: NB - FE - S
> Building proper torsion parameters.
>
So you have already created the frcmod file? I suggest using parmchk to
build the frcmod file. That will fill in values for every parameter you
need (if it can't find out what they should be, you get a helpful message
and a holder for that parameter).
Is it appropriate to us the parmaters provided in the Charmm paramater
> files ..?
>
No. They are different potentials that were parametrized differently. You
can't assume they can be combined unless validated.
> Can anybody please provide the frcmod and prepin files or suggest me how to
> go about ..?
>
I would search the literature to see if anybody has simulated a system with
a similar (or the same) cofactor. There is also a database of Amber
parameters here: http://www.pharmacy.manchester.ac.uk/bryce/amber that
might have something that will help you.
HTH,
Jason
>
> Thank you
> Gurunath
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Mar 24 2012 - 09:00:02 PDT
