Hi Musa,
Could you do the following things for me?
1) please specifiaclly list here all .PB parameters you use in your mmpbsa.in file to run your mmpbsa jobs.
2) rerun mmpbsa only for 2 snaphosts of the complex or receptor or ligand species..and send me $PREFIX_com.all.out or $PREFIX_rec.all.out or $PREFIX_lig..all.out (where $PREFIX is the prefix you use)
I'll run a few test jobs at the TR-GRID facility of Turkiye to see if we get similar error messages. If we don't, then i would recommend that you replace all mmpbsa source codes in your $AMBERHOME/src/mmpbsa directory with fresh ones and rerun mmpbsa.
3) I hope that you are not currently using TR-GRID for your MMPBSA exps because I have been currently (and temporarily) modifying some mmpbsa codes for some users at TR-GRID to be able to run it in parallel. If you are using TR-GRID for MMPBSA jobs , please let me know...
cheers,
Jenk
musa özboyacı <musaozboyaci.gmail.com> wrote: Dear Jenk,There appears nothing wrong with the output, and it did not give
any error. Indeed. The "ELRAELE" problem was occuring while statistics
calculations. I guess there is something wrong in statistics code and the
same problem does not happen in GB calculations.
Best regards,
Musa
2009/1/25 Cenk (Jenk) Andac
> Hi Dave,
>
> "David A. Case" wrote:
>
> Just a extra note here: cutcap, xcap, etc. *are* in the &cntrl namelist
> for sander, but not for pbsa. I don't know which program mm_pbsa is
> calling with this input.
>
> Bottom line: the original error may have a very different origin than
> the one I suggested.
>
> ...dac
>
> Thanks for reminding me about using sander in MMPBSA v10.
> I have MMPBSA versions 8 through 10 installed on my computer and I
> sometimes forget what version goes with what.
>
> So, Musa may want to retry the previous pbsa.in using SANDER v10 as
> follows:
>
> sander -O -i pbsa.in -o pbsa.out -p prmtop -c snapshot1.x
>
> I wonder now how pbsa.out will come out.
>
> cheers,
>
> jenk
>
>
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Received on Wed Jan 28 2009 - 01:08:50 PST
