then you should look at how you built the structure since it has a
problem. you might want to minimize it first- that may solve the
problem. it will also show you which atom has the highest gradient,
and you can you a viz program to inspect that region.
On Tue, Oct 21, 2008 at 7:28 AM, Urszula Uciechowska
<urszula.uciechowska.pharmazie.uni-halle.de> wrote:
>
> I just checked it but also with ntr=0 error is the same
>
> Urszula
>
>
>> have you tried with ntr=0? that will help narrow down the source of
>> the problem.
>>
>>
>> On Tue, Oct 21, 2008 at 7:17 AM, Urszula Uciechowska
>> <urszula.uciechowska.pharmazie.uni-halle.de> wrote:
>> > yes the inpcrd is the same as the refc,
>> > i changed the mask to restraintmask=':1-300.CA', restraint_wt=10
>> > but the error is still the same:
>> >
>> > Coordinate resetting (SHAKE) cannot be accomplished,
>> > deviation is too large
>> > NITER, NIT, LL, I and J are : 0 0 68 4641 4639
>> >
>> > Note: This is usually a symptom of some deeper
>> > problem with the energetics of the system.
>> >
>> > Urszula
>> >
>> >
>> >
>> >> is the inpcrd the same as the refc?
>> >> the mask looks odd- have you carefully checked the sander output to
>> >> make sure it selects what you want?
>> >>
>> >>
>> >> On Tue, Oct 21, 2008 at 6:44 AM, Urszula Uciechowska
>> >> <urszula.uciechowska.pharmazie.uni-halle.de> wrote:
>> >> > Dear amber users,
>> >> >
>> >> > I am trying to equilibrate the total volume of the water box for
>> 20
>> >> ps, at constant pressure (1atm) and
>> >> > constant temperature (300K), and with positional restraints for CA
>> >> and the crystal waters.
>> >> > the input file:
>> >> > &cntrl
>> >> > imin = 0, irest = 0, ntx = 1,
>> >> > ntb = 2, pres0 = 1.0, ntp = 1,
>> >> > taup = 2.0,
>> >> > cut = 9, ntr = 1,
>> >> > ntc = 2, ntf = 2,
>> >> > tempi = 300.0, temp0 = 300.0,
>> >> > ntt = 3, gamma_ln = 1.0,
>> >> > nstlim = 25000, dt = 0.002,
>> >> > ntpr = 50, ntwx = 50, ntwr = 50
>> >> > restraintmask=':1-300.CA&:4799-40288', restraint_wt=10
>> >> > /
>> >> > I am getting such a error:
>> >> >
>> >> > Coordinate resetting (SHAKE) cannot be accomplished,
>> >> > deviation is too large
>> >> > NITER, NIT, LL, I and J are : 0 0 68 4641 4639
>> >> >
>> >> > Note: This is usually a symptom of some deeper
>> >> > problem with the energetics of the system.
>> >> >
>> >> > Could somebody help me to track the problem?
>> >> >
>> >> > Urszula
>> >> >
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Received on Wed Oct 22 2008 - 05:10:03 PDT
