Hi,
I recommend that we add some tests for mm_pbsa.
I have had to modify various parts in response to user issues at OSC.
Im batting about 50% in making silly mistakes, and because testing is not
as trivial as cd test;make mm_pbsa, this usually takes an extra cycle
with the user finding my mistake.
Probably this goes on the wiki, but email is so much easier.
thanks,
Scott
ps Details:
Here's today's silly mistake:
Undefined subroutine &main::calc_energy_entropy called at
/usr/local/amber/current/src/mm_pbsa/mm_pbsa_pbsacutres16.pl line 67
which was caused by not changing the perl package name when changing
the file name; perl could be more helpful here.
Here are the kinds of changes that I have made:
diff mm_pbsa_calceneent.pm.original mm_pbsa_calceneent_Fradius1_verbose.pm
9c9
< package mm_pbsa_calceneent;
---
> package mm_pbsa_calceneent_Fradius1_verbose;
389,391c389,393
< unlink $sanout;
< unlink $sanres;
< unlink $nmodeout;
---
> # modified for ticket 10251
> print " Notice: keeping sander output, sander restart, and nmode output files.\n";
> #unlink $sanout;
> #unlink $sanres;
> #unlink $nmodeout;
438a441
> "F" => 1.000 + 1.400,
447a451,452
> print " Warning: the fluorine radius is 1.0 Angstroms.\n";
> print " This warning only applies to MS=1 calculations.\n";
diff mm_pbsa_createinput.pm mm_pbsa_createinput_cutres16.pm
9c9
< package mm_pbsa_createinput;
---
> package mm_pbsa_createinput_cutres16;
433a434,436
> # modified for ticket 9249:
> print " Using PBSA non default cutres of 16\n";
> print OUT " cutres = 16\n";
Received on Wed Oct 04 2006 - 06:07:23 PDT
