you may be able to use ptraj to obtain input coordinates
in a restart format, as long as the trajectory file is ok.
you won't have velocities but if you set tempi=0 and ntx=1
then sander will generate velocities from the forces.
the ptraj script looks ok. I'm not sure why you image if
you're stripping the water. the image command has lots of
options, I usually use it with the "center" option. try removing the
image command and see if that helps.
lucas luquitas wrote:
> Ok, thanks Carlos!
> I checked it, if I understood well the idea to solve this is to wrap
> the waters, setting iwrap=1, be sure to have nscm=xxstep. I prefered
> to wrap my system when I analyse
> my simulations as I never had this problem.
> What I could not find is there is any posibility of restarting the
> run, I can imagine
> using the velocity information writing the rst coordinates using ptraj
> or rdparm?
>
> Regarding the image problem, here is my simple ptraj script:
>
> trajin .protein1crd
> trajout protein2.crd
> rms first out rms .CA,C,N
> center :1-33
> image
> strip :WAT
> go
>
> Lucas
>
> On 2/20/06, Carlos Simmerling <carlos.simmerling.stonybrook.edu> wrote:
>
>> search for restart and iwrap on the amber web page search bar (search
>> mail list).
>> the results of image/center/strip depends on what you ask ptraj to
>> do. Since you didn't tell us that it's hard to help. Check the archives,
>> this has been discussed before.
>>
>> lucas luquitas wrote:
>>
>>
>>> Hi all,
>>> I am ruuning a normal constant temperature simulation of small protein(34aa) in
>>> a periodic box of TIP3P waters. The simulation is quite long around
>>> 80ns, the problem
>>> is when I want to restart the simulation, my restart file is corrupted!!
>>> When I check, I see that some of the coordinates are above 1000, so it
>>> prints ***********.
>>> The other thing is that when I image and center and strip to view the
>>> traj with VMD, I see jumping in the coordinates, like if it were
>>> moving between boxes!
>>>
>>> Here is the inp file:
>>> &cntrl
>>> imin=0,
>>> ntc=2, ntf=2,
>>> cut=12.0,
>>> ntpr=500, ntwx=10000, ntwv=10000,ntwe=500,
>>> nstlim=90000000, dt=0.002,
>>> ntt=1, tempi=300.0, temp0=300.0, tautp=1.0,
>>> ntx=5, irest=1, ntb=2,
>>> ntp=1, PRES0=1, TAUP=1,
>>> nscm=10000,
>>> ntr=0,
>>> &end
>>>
>>>
>>>
>>> Lucas
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>>>
>>>
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Received on Sun Feb 26 2006 - 06:10:10 PST
