Dear Jason Swails
Thanks for your attention
In min_v1.in file, crgmask defined twice, Because I want to
investigate free energy changes in mutation of the dna (GC base pair
---> AT base pair). one for G base and the other for C base.
how to define crgmask only once?
You should probably put masks in quotes.
crgmask = ":DG9.O6,H1,N2,H21,H22"
is it true?
On 2/6/12, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 10:30:05 PST
