that error is probably not related to the wrapping.
Have you looked at the prod3.rst file to make sure it exists and is not
currupted?
if you want help with file issues, also send the scripts that show the file
names for each step.
On Mon, May 2, 2016 at 7:57 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
wrote:
> I did all atom simulation of my protein-ligand complex on 2 GPUs (Tesla
> M2090). Here is my input file:
>
> All atom simulation
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 5,
> ntb = 2,
> ntp = 1,
> cut = 8.0,
> ntc = 2,
> ntf = 2,
> tempi = 298.0,
> temp0 = 298.0,
> ntt = 3,
> taup = 2,
> ig = 47123,
> iwrap = 1,
> gamma_ln = 1.0,
> nstlim = 35000000, dt = 0.002
> ntpr = 1000, ntwx = 1000, ntwr = 50000
> &end
>
>
> After 13399000 steps, simulation stopped and I got following error in
> output file:
>
> "Unit 16 Error on OPEN: prod3.rst"
>
> When I generated the pdb file using ambpdb, I observed that proteins are
> ligands are outside the water-box (see attached image).
>
> Can anyone suggest me what am I doing wrong.
>
>
>
>
>
> *​Thanks,Hirdesh​*
>
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>
>
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Received on Mon May 02 2016 - 05:30:03 PDT
