On Mon, Feb 11, 2013 at 5:17 PM, Adam Mepham <amepham.sympatico.ca> wrote:
> This is an addition to the email sent on Sat, Feb 9. Unfortunately I
> did not receive the response of Daniel Roe, so I am unsure how to
> continue that thread.
> I am simulating the pKa of residue in a protein, and I wish to know in
> what manner each residue is contributing to energy changes. My input
> file is as follows:
>
>
> &cntrl
> nstlim =1, nscm=2000,
> ntx=1, irest=0, ntpr=1000,
> tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
> ntb=0, igb=5, cut=999.0,
> dt=0.001,
> idecomp=1,
> ntc=2, ntf=2,
> ntwr = 10000, ntwx=1000, ntave=1000
> /
> All Residues
> RES -1 124
> END
> END
>
-1 should be 1, correct?
Also, try adding a RRES record. So something like this:
Residues as receptor
RRES 1 124
END
Residues to print
RES 1 124
END
END
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Feb 11 2013 - 15:00:02 PST
