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,
Ray
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
>
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--
====================================================
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: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Thu Apr 15 2004 - 19:53:00 PDT
