AMBER Archive (2004)

Subject: Re: AMBER: Amber7 - mm_pbsa/molsurf

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Fri Sep 10 2004 - 13:03:57 CDT

Hi Nadine,

I encountered the same errors for a few of my several hundred snapshots
with mm-pbsa and amber_8_ - so this has nothing to do with the version
of amber. I also did not have to increase MAXAT for running mm_pbsa, so
the problem is also not related to your increased MAXAT value. I guess
the best workaround is to skip the sanpshots for wich molsurf is unable
to calculate the surface(?). Of course it would be nice to know what's
going on...

Best,
Oliver

Nadine Homeyer wrote:
> Dear all,
>
> I'm trying to perform an MM/PBSA analysis of a rather big protein
> complex using Amber7.
> After first increasing the MAXAT parameter of molsurf in molsurf.h and
> recompiling the program I obtained a result via mm_pbsa.pl.
>
> However, inspection of the mmpbsa.log file reveiled that the molecular
> surface was not be calculated for each snapshot (WARNING: "Missing SURF
> for MS in x -> Taken from x-1"). In the output files of molsurf (mslog)
> I found the following two errors: "two many interesecting cusps 5" and
> "reroute(): cusp edge mismatch". Additionally, molsurf produced the
> error "make_cones() MAXTOR_PROBE exceeded". Looking into the source code
> I found that this is probably no trivial problem...
>
> Has anybody faced these problems before? Are they somehow connected to
> the increased value of MAXAT? Would an upgrade to Amber8 solve the problem?
> I would very much appreciate any helpful comments!
>
> Best regards,
>
> Nadine Homeyer
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-- 
_______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke_at_u.washington.edu
_______________________________________________________________

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