Dear amber users,
I'm having trouble convincing myself that the ptraj action
principal mask
actually aligns the principal axes of the selection with the coordinate axes (this is qhat is suppose to do, right?)
In particular if one picks out a phenol ring (or any ring for that matter) and aligns the carbon atoms one would expect that the ring will end up in say the x-y plane or y-z plane or z-x plane. Granted for such rings two of the principal axes will be close to degenerate so there may be some trouble, but ptraj should be able to handle this.
NOTE: in my copy of action.c the "DoRotation" value is came set to 0 during the principal action.
I set DoRotation to 1 and recompiled but that does not cause the alignment that I expect either.
In a related issue. I am not convinced that the ptraj action
vector name mask {principal [| x| y| z|] } | dipole| mask2|box} [ out filename}
is calculating the principal axes correctly either.
Again a simple test on a ring does not produce 2-vectors in the plane of the ring and one perpendicular to this plane.
Can someone help me figure this out.
(script details listed below)
Thanks,
Tom
Here's basically all my ptraj script contains (other than a trajin )
where 242 is the resid of my phenol and C1... are the atomsnames.
vector princ :242_at_C1,C2,C3,C4,C5,C10 principal x out analy/lig-px.dat
vector princ :242_at_C1,C2,C3,C4,C5,C10 principal y out analy/lig-py.dat
vector princ :242_at_C1,C2,C3,C4,C5,C10 principal z out analy/lig-pz.dat
I would also expect that
trajin A.in.crd
trajout A.out.crd
principal .CA
would align the principal axes of the backbone of my protein w/ the x,y,z axes and make a new trajout.
-----------------------------------------
Thomas C. Bishop, PhD.
Center for Bioenvironmental Research
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Tulane University Office
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Dept. of Environmental Health Sciences(SL-29)
School of Public Health & Trop. Medicine
1430 Tulane Avenue
New Orleans, LA 70112
Phone: 504-988-6203 Fax: 504-585-6428
bishop_at_tulane.edu
-----------------------------------------
Xavier University Office
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Division of Basic Pharmaceutical Sciences
College of Pharmacy
7325 Palmetto Street
New Orleans, LA 70125
Phone: 504-485-5106 Fax: 504-485-7930
tbishop_at_xula.edu
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Received on Wed Jul 18 2001 - 06:23:30 PDT
