Hi,
I would like to calculate the protein COM from my amber12 simulation. the
protein was autoimaged and rms fitted to a reference structure. The command
I'm using is:
vector v0 center :1-68.N,CA,C,O :1-68.N,CA,C,O out prot_COM.dat
The command seems to work and I get the output included below. However,
from looking at the mailing list, the COM is meant to be the second set of
three numbers. see
http://archive.ambermd.org/201302/0377.html
However, the output is not the same as that in the link above. Not sure if
I have fully understood the vector command properly. If someone could
hopefully offer some guidance that would be great!
########################################
#Frame v0
1 34.3814 32.3427 27.5217 0.0000 0.0000 0.0000
2 34.3852 32.3313 27.5320 0.0000 0.0000 0.0000
3 34.3806 32.3322 27.5277 0.0000 0.0000 0.0000
4 34.3855 32.3349 27.5257 0.0000 0.0000 0.0000
5 34.3868 32.3368 27.5282 0.0000 0.0000 0.0000
6 34.3835 32.3379 27.5248 0.0000 0.0000 0.0000
7 34.3799 32.3291 27.5326 0.0000 0.0000 0.0000
8 34.3786 32.3375 27.5250 0.0000 0.0000 0.0000
9 34.3779 32.3353 27.5360 0.0000 0.0000 0.0000
########################################
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Received on Tue Apr 07 2015 - 08:00:03 PDT
