On Mon, Aug 29, 2016, 张姝姝 wrote:
>
> I am trying to do the tutorial of TI calculation. I have downloaded all
> the setup files and followed the steps in the "sander" fold.
> I went through the minimization, heat, press steps for ligands,
> but errors came out when pressing for the complex, while the heating
> steps for complex seem to finish normally.
> "vlimit exceeded for step 673; vmax = 48.8156
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 3 239 474 473
>
> Amber 12 SANDER 2012
It is possible that some bug has been fixed since Amber12: if the ideas
below don't help, consider upgrading to AmberTools16. Note that you probably
should be looking at the "old version" of the tutorial (linked at the bottom
of the first page.)
> NATOM = 30532 NTYPES = 17 NBONH = 29228 MBONA = 1316
I'm a little lost here: None of the complex files in the T4-lysozyme tutorial
(tutorial A9) have this number of atoms. Can you be more explicit about
exactly which tutorial you are trying to run? Have you made changes to it?
> Softcore Mask :1.H6; matches 1 atoms
> this run corresponds to V0, its softcore atoms interact fully for lambda=0
> this process: 30532 atoms, partner process: 30533 atoms
> Checking for mismatched coordinates.
> WARNING: Local coordinate 8034 differs from partner coordinate 8037 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 8037 differs from partner coordinate 8040 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 8040 differs from partner coordinate 8043 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 11418 differs from partner coordinate 11421 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 11421 differs from partner coordinate 11424 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 11424 differs from partner coordinate 11427 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 11454 differs from partner coordinate 11457 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 11457 differs from partner coordinate 11460 !
> Deviation is small, changing partner coordinate.
> WARNING: Local coordinate 11460 differs from partner coordinate 11463 !
> Deviation is small, changing partner coordinate.
> ... making more adjustments ...
> A total of 987 small coordinate adjustments were made, check results carefully.
> Molecule 1 is partially softcore on this side or the corresponding partner molecule is.
> Checking for SHAKE constraints on bonds crossing into the SC region
> Removing shake constraints from H6 BNZ 1 -- C6 BNZ 1
The above messages are disturbing, although maybe others will know if they
should be found.
> | MULTISANDER: 2 groups. 8 processors out of 16 total.
Try just using mprun -np 2: it's possible that something funny is happening
in parallel.
....dac
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Received on Mon Aug 29 2016 - 12:30:03 PDT
