AMBER Archive (2001)

Subject: sander input in Amber 6

From: Anton B. Guliaev (anton_at_vostok.lbl.gov)
Date: Fri Aug 17 2001 - 10:14:32 CDT

Dear Amber Users:

I posted this question earlier but it looks like it never made it to the reflector due to
shut down. My question was: Can I specified the box size in the md.in together with
the Group constraints in sander (amber 6.0) the same why you do in sander_classic.
&cntrl
ntx=1, nirest = 0, mropt=1, ntr=1, .............
&end
69.8099659 62.0682638 86.6690242 90.0 90.0 90.0
75 68 90 4 0 0 0
0.00001
Allowing only solvent to move
300.0
RES 1 345
END
END

In my case the new sander thinks that the first line is a group restraint rather the size
of the box and immediately crashes... If I use ntr=0, than it takes it fine, but I loose
my group restraint....

Thanks a lot ,

Anton
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