Dear Amber users,
I am trying to parameterize an organic molecule (109 atoms), and in the step
$AMBERHOME/bin/prepgen -i receptor_resp_gaff.ac -o receptor_resp_gaff.prepc -f car
I obtain an incorrect prepc file, where all the atoms after 37 have lines filled from zeros.
0 0 2
This is a remark line
molecule.res
MOL XYZ 0
CHANGE OMIT DU BEG
0.0000
1 DUMM DU M 999.000 999.0 -999.0 .00000
2 DUMM DU M 999.000 -999.0 999.0 .00000
3 DUMM DU M -999.000 999.0 999.0 .00000
4 C13 c2 M -1.463000 4.538000 2.303000 -0.117501
(...)
36 H18 hc E -9.404000 3.700000 4.423000 0.023308
37 H19 hc E -10.004000 5.386000 4.547000 0.023308
38 X 0.000000 0.000000 0.000000 0.000000
39 X 0.000000 0.000000 0.000000 0.000000
40 X 0.000000 0.000000 0.000000 0.000000
41 X 0.000000 0.000000 0.000000 0.000000
42 X 0.000000 0.000000 0.000000 0.000000
(...)
In the file "receptor_resp_gaff.ac" all these lines are correctly completed.
Any idea of why is this happening?
Best wishes,
Rebeca.
Dr. Rebeca Garcia
Santiago de Compostela University
Spain
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Received on Thu May 07 2015 - 08:00:03 PDT
