AMBER Archive (2004)

Subject: Re: AMBER: pbsa

Date: Thu Apr 15 2004 - 13:14:34 CDT

Hi Chenlong,

If you're using radiopt=1 to ask pbsa to set radii for you, you have to
use amber standard atom types, i.e. gaff atom types are all in lower
case. pb_init does not recognize these extended atom types that Junmei
proposed in the gaff force field. radiopt=1 and 2 are for proteins only
right now, and these will eventually go to leap in future releases.

I suggest that you get the radii yourself into prmtop for small
molecules using a perl script. The default rules for radiopt=1 are the
following as copied from the "pb_init" file.

       ! all H on sp3 C : 0.00 A
       ! all H charged or on N : 1.10 A
       ! all other hydrogens : 1.20 A
       ! all sp3 C : united radii 2.29 A
       ! all other heavy atoms : (sigma+sprob)/2

If possible, refine your radii starting from the default values
according to experimental solvation free eneriges. These are done for
all natural amino acids when radiopt=1 or 2. Let me know if this can
solve your problem.

All the best,

Chenglong Li wrote:
> Hi,
> I'm experimenting pbsa with RADIOPT=1 in amber8 and found:
> a) if small moleclue included either alone or with protein, PB bombed
> with "pb_aaradi(): ZERO sigma found for non-hydrogen atom";
> b) if protein alone, PB initialization passed, but bombed next with
> "pb_reslist(): maxnbr too small".
> so it looks that there is problem with small molecule prmtop generated
> with antechamber/gaff/leap(?). And how about maxnbr? Increase cutres
> because maxnbr = natom * (sqrt( cutres + 3.0d0 ))**3 / 3.0d0?
> Thanks for help,
> Chenlong
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" to
> .

Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
Home page:

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to