On Wed, 2014-08-13 at 17:57 +0200, Hirdesh Kumar wrote:
> I also faced the same problem. I ran 100ns simulation of my
> protein-ligand-ion complex in TIP3P. I found that the rmsd value for ligand
> is not stable so thought of continuing the simulation. But I can not use
> the restart file.
>
> I got following error:
> ERROR: I could not understand line 22288
> 119.5803932 241.7497484-572.4462595
>
>
> I opened the previous restart file and checked for this line. I found that
> usually there are 6 coordinates in a line (for 2 atoms, if I am not wrong).
> But in the error line there is only 3 coordinate information..
How many atoms do you have in your system? If you have an odd number of
atoms, then you will have at least 1 line with only 3 numbers.
>
> 32.4272362 107.0995698 73.2442804 31.4632046 106.0229371 72.7942916
> 120.3886214 242.0088540-572.8888241 121.0825779 241.7930826-572.2658482
> 119.5803932 241.7497484-572.4462595
> -0.0167718 -0.0424197 -0.0394365 0.1475965 0.5324544 0.2035670
> 0.2566837 -0.1595890 -0.0562660 -0.0466537 0.0079685 -0.1094048
>
>
> I tried to generate the pdb file from last restart file (using ambpdb) but
> it also showed some error.
>
> As an alternative, I took previous trajectory file (prod1.crd) and I tried
> to generate the restart file after 50 ns simulation. I managed to generate
> the restart file (also ambpdb worked with with this new restart).
>
> BUT, when I restarted my simulation with this restart file, I got following
> error:
>
> *ERROR: I could not find enough velocities in restart1.rst*
>
>
> As Dac suggested, I can use the netcdf format in future. But please let me
> know how to restart this simulation 100ns onward???
My guess is that the restart file you printed doesn't have any velocity
information in it, but you still set irest=1, ntx=5 in your input file.
This tells sander to use the velocities in the restart file. When they
can't be found, sander complains. So the solution is to use ntx=1,
irest=0 to regenerate velocities from a M-B distribution.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 13 2014 - 09:30:02 PDT
