AMBER Archive (2004)

Subject: AMBER: Amber7 - mm_pbsa/molsurf

From: Nadine Homeyer (
Date: Fri Sep 10 2004 - 07:25:20 CDT

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

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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