> Thanks for your answer.
> I modified the lines you told me in the file freemol/src/mengine/field.h
> (not field.c). Now the clean command works (altought there is no message
> indicating the finalization of the minimization).
Great, I'm glad that worked. And, yes, you're correct, I meant
"field.h" not "field.c". Input into mengine is done via stdin and
output via stdout:
./mengine < my_test.sdf
> I one more question, Where I can find more information on the clean command?
> It is possible to change parameters like number of cycles, type of
> minimizer, nonbonded cutoff-interaction (without recompiling)?
> How much difficult would be to implement in PyMOL another forcefield like
> Amber, OPLS etc?
You can't change those without recompiling. "./mengine.exe -h" will
give you help on what you can change. Be warned that this code was
used in another package and so even that help message might be
Regarding implementation effort, the mengine code might give you a
hint. But, hooking up a different extant binary should be as easy as
plugging in a new forcefield that takes SDF input and returns SDF
output. Eg, if you symbolically linked a different binary to
'mengine.exe' PyMOL wouldn't be the wiser.
> On Fri, Oct 12, 2012 at 12:49 PM, Jason Vertrees
> <jason.vertrees@...> wrote:
>> Hi Osvaldo,
>> > when I run the clean command (I tried with different molecules and file
>> > formats) I get
>> > Cleaning 176 atoms. Please wait...
>> > *** buffer overflow detected ***: /opt/freemol/freemol/bin/mengine.exe
>> > terminated
>> Thanks for being patient on this, I just now had time to look at this.
>> Please edit the file freemol/src/mengine/field.c, at line 7, and
>> char vdwtype
>> char vdwtype
>> Once you've done that, please remove all the .o files and rebuild
>> mengine. If this helped you, let me know and I can update freemol.
>> -- Jason
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrödinger, Inc.
>> (e) Jason.Vertrees@...
>> (o) +1 (603) 374-7120
Jason Vertrees, PhD
PyMOL Product Manager
(o) +1 (603) 374-7120