AMBER Archive (2009)

Subject: Re: [AMBER] MM - PBSA problem

From: musa özboyacı (musaozboyaci_at_gmail.com)
Date: Sun Jan 25 2009 - 07:12:05 CST

Dear Jenk,
I tried the way you suggested, it gave me the following error :

At line 657 of file _mdread.f (Unit 5 "pbsa.in")
Traceback: not available, compile with -ftrace=frame or -ftrace=full
Fortran runtime error: In line 1 of namelist cntrl:
Namelist variable 'cutcap' not found
  cutcap
        ^
After deleting cutcap variable the same error appeared for xcap, ycap and
zcap. Then I deleted all and it gave me an output without any error
messages.But I am not sure whether this causes those errors!
I also tried the mm-pbsa module in Amber8. It gave me all the outputs
without any "ELRAELE" errors. I guess this is a bug of Amber10. Anyway,
thank you and other guys for your helps.

Best regards,

Musa

2009/1/23 Cenk (Jenk) Andac <cenk_andac_at_yahoo.com>

> Hi Musa,
>
> you may also want to use the following input to run a standalone pbsa job
> as follows.
>
> pbsa -O -i pbsa.in -o pbsa.out -p prmtop -c snapshot1.x
>
> pbsa.in
> File generated by mm_pbsa.pl. Using PB
> &cntrl
> ntf = 1, ntb = 0,
> igb = 10, dielc = 1.0,
> cut = 999.0, nsnb = 99999,
> scnb = 2.0, scee = 1.2,
> imin = 1, maxcyc = 0, ntmin = 2,
> ivcap = 0, cutcap = -1,
> xcap = 0, ycap = 0, zcap = 0
> idecomp= 0,
> &end
> &pb
> epsin = 1.0, epsout = 80,
> istrng = 0, radiopt = 0,
> sprob = 1.4, space = 0.5,
> maxitn = 1000, npopt = 1, dbfopt = 1,
> cavity_surften = 0.0072, cavity_offset = 0.00,
> npbverb= 1
> &end
>
> make sure that the prmtop and coordinate files do not include water
> molecules and ions.
> pbsa.in given above is generated by the mmpbsa module.
> pbsa.out will exactly tell what the problem is. It would be helpful if you
> can share your pbsa.out with us.
>
>
> cheers,
>
> jenk
> musa özboyacı <musaozboyaci_at_gmail.com> wrote: Dear All,Thank you very much
> for your suggestions. I tried the way which
> Jenk suggested, but it gave me same output ever time I tried. There is no
> problem with GB part. For the way that Niel suggested, well I am not
> allowed
> to change the code. But if this is a bug than I could find a way to change
> it. The guy who suggested to change the part in the code, actually is not
> sure whether it is a safe way or not.
>
> "By changing index 0 of ELRAELE, EPB, PBNONPOL to 0, MM-PBSA would
> complete. Can anyone tell me if this was a valid way of solving the
> problem or have I misunderstood something. "
>
> One more thing : Is there any one, who really knows what this ELRAELE
> parameter stands for?
>
> Best regards,
>
> Musa
>
>
>
> 2009/1/23 Niel Henriksen
>
> > Hi Musa,
> >
> > >Dear Amber users,
> > >I've trying to use mm-pbsa tool of AMBER, and everytime I use I get the
> > same
> > >error. I tried every possible suggestions in the old mails. However I
> > >couldn't fix the problem. I would be very glad if you help me. Here is
> my
> > >output:
> >
> > >........
> > >=>> Calc delta from raw data
> > > No data for 0+0 PB ELRAELE 0
> >
> > If Jenk's suggestion doesn't work, here is another idea.
> >
> > I think you may be having a problem that has been reported before. I had
> a
> > similar issue and I used the fix described here:
> > http://archive.ambermd.org/200806/0357.html
> >
> > I don't think there has been an "official" response as to whether this
> fix
> > is valid or not, so use at your own risk (I vaguely remember success at
> > comparing results from amber9 with amber10).
> >
> > -niel
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> >
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