AMBER Archive (2009)

Subject: Re: [AMBER] MM - PBSA problem

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Fri Jan 23 2009 - 08:34:46 CST

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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