AMBER Archive (2009)

Subject: Re: [AMBER] MM - PBSA problem

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Mon Jan 26 2009 - 06:14:52 CST

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_at_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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