Re: [AMBER-Developers] recent PB changes?

From: Mengjuei Hsieh <>
Date: Fri, 5 Feb 2010 11:47:09 -0800

On Fri, Feb 05, 2010 at 01:16:30PM -0500, Jason Swails wrote:
> Hello, It appears as though some changes have been made in the PBSA
> that have broken input files we've been using for MMPBSA. The input
> file is shown below, along with the error in mdout that it gave.
> Any ideas? -------------------------------------------------------
> PB Info in pb_read(): igb has been overwritten by ipb
> PB Info in pb_read(): npopt has been overwritten with inp
> PB Bomb in pb_read(): use of radi other than vdw sigma for
> np solvation dispersion/cavity is not supported!

Hi Jason,

Here are some of my first impressions of the problem, more details
to come later today.
  The first warning is perplexing since the default ipb shouldn't
     have different meaning of igb=10. It possibly is a bug.
  The second warning is due to the default inp value, I am not sure
     which method MMPBSA is supposed to use to compute non-polar
     solvation free energy. Ref: The AmberTools document.
  The bomb can be explained in the same paragraph of above reference,
     as to the appropriate update to mdin, allow me discuss this with
     Ray and Irvine people.

Mengjuei Hsieh, Luo Research Group, Molecular Biology & Biochemistry,
University of California Irvine.
On Fri, Feb 05, 2010 at 01:16:30PM -0500, Jason Swails wrote:
>  &cntrl
>    ntb=0, igb=10, cut=999.0, nsnb=99999,
>    imin=5, maxcyc=0, cutcap=-1, xcap=0,
>    ycap=0, zcap=0, idecomp=0, ntpr=1,
>    ivcap=0, ntmin=2,
>  &pb
>    dbfopt=1, epsin=1, epsout=80, istrng=100.0,
>    radiopt=0, sprob=1.4, space=0.5, maxitn=1000,
>    npopt=1, cavity_surften=0.00542, cavity_offset=-1.008,
>    fillratio=4,
AMBER-Developers mailing list
Received on Fri Feb 05 2010 - 12:00:02 PST
Custom Search