Hello,
The RRES, LRES, RES cards have to come after the &cntrl namelist, not inside
it. They also each need a title, as explained in a recent post. Change
your mdin file as such:
mdin file
&cntrl
... list variables here ...
/
Receptor residues
RRES # #
END
Ligand residues
LRES # #
END
END
Or something to that effect. You can also use mm_pbsa.pl to automatically
create the input files.
Good luck!
Jason
On Thu, Aug 19, 2010 at 3:05 PM, g t <sketchfoot.gmail.com> wrote:
> Hi, please excuse me as I do not have a lot of experience with AMBER. I
> have
> been finding the correct syntax to use for per residue decomposition. I am
> using amber 10 with the mpi version of sander. I cannot find any example of
> using RRES cards with sander in the manual.
>
> my input file for the production run looks like this:
>
> NPT
> production
> &cntrl
>
> imin = 0, ntx = 5, irest =
> 1,
> ntpr = 10, ntwr = 1000, ntwx =
> 0,
> ntf = 2, ntc =
> 2,
> ntb = 2, cut =
> 9.0,
> nstlim = 1000, dt =
> 0.002,
> temp0 = 300.0, ntt = 3, gamma_ln =
> 2,
> ntp = 1, pres0 = 1.0, taup =
> 2.0,
> icfe=1, clambda =
> 0.1,
> idecomp =
> 2,
> RRES 1
> 10
> RES 1 10
>
>
> ifsc=0,
>
>
> crgmask='',
>
> &end
>
> I have tried a variety of other variations, but always get the message "
> error in reading namelist cntrl". If anyone could help me with my syntax, I
> would be obliged.
>
> best regards,
> GT
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Aug 19 2010 - 12:30:05 PDT
