Dear users,
I am calculating contacts between a protein-protein complex in a
trajectory using nativecontacts command from ambertools14. In the manual,
it has been specified that the map file written has values normalized to
1.0 (can i assume it is from 0 to 1 depending on their lifetime occurrence
during trajectory??)
i have used this command:
nativecontacts :1-974 :976-1143 writecontacts p1_p2_contacts.dat distance
5.0 out p1_p2_cont_num.dat first name p1-p2 byresidue map mapout
p1_p2_map.dat
in the map file, i am getting some values which are negative, and some are
way beyond 1.0..like-
===============
805.000 1095.000 -0.0525
808.000 1095.000 -2.5484
851.000 1095.000 -1.6074
852.000 1095.000 -1.0348
853.000 1095.000 -22.9172
854.000 1095.000 -0.0344
856.000 1095.000 -0.0190
904.000 1095.000 -1.9920
...
...
...
796.000 1143.000 13.4246
797.000 1143.000 8.0078
798.000 1143.000 1.6831
799.000 1143.000 2.3897
==================
I don't think these are normalized values and why negative values are
coming?? Can you please explain what's going wrong here..
Thanks
Asmita
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Received on Tue Nov 11 2014 - 09:30:02 PST
