On Mon, Feb 6, 2012 at 10:36 AM, leila karami <karami.leila1.gmail.com>wrote:
> Dear amber users
>
> I am trying to perform thermodynamic integration using soft core potentials
> (like tutorial A9).
>
> I want to investigate free energy changes in mutation of the dna (GC base
> pair ---> AT base pair).
>
> I do first step (removing charge of G9 and C18).
>
> But after mpirun -np 4 $AMBERHOME/exe/sander.MPI -ng 2 -groupfile
> min.group,I am faced with
> the error in reading namelist cntrl.
>
> my input files are as follows:
>
> min_vo.in
>
> &cntrl
> imin = 1, ntx = 1,
> maxcyc = 2000, ncyc = 1000,
> ntpr = 100,
> ntf = 2, ntc = 2,
> ntb = 1, cut = 10.0,
> icfe = 1, clambda = 0.1
> ifsc = 0,
> crgmask ="
> scmask ="
> /
>
> min_v1.in
>
> &cntrl
> imin = 1, ntx = 1,
> maxcyc = 2000, ncyc = 1000,
> ntpr = 100,
> ntf = 2, ntc = 2,
> ntb = 1, cut = 10.0,
> icfe = 1, clambda = 0.1
> ifsc = 0,
> crgmask = :DG9.O6,H1,N2,H21,H22
> crgmask = :DC18. N4,H41,H42,H5
>
Why do you have crgmask defined twice? Also, you should probably put masks
in quotes (single or double, I don't think it matters).
> scmask ="
> /
>
> Any help will highly appreciated.
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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 Mon Feb 06 2012 - 08:00:03 PST
