Re: AMBER: (no subject)

From: Thomas E. Cheatham, III <>
Date: Thu, 24 Jul 2003 10:32:28 -0600

> > TRAJ: dihedral zx .H64,C29,C30,H66 ph2
> > Mask [.H64,C29,C30,H66] represents 4 atoms
> > WARNING: Error in mask string,no "." or ":" present (ph2)
> I assume that you wanted to write the results to the "ph2". For this,
> you have to specify "out" as a keyword in front of the name (see the
> dihedral command in the manual):
> dihedral zx .H64,C29,C30,H66 out ph2

Further, you need 4 *separate* atom masks as all the commands like
distance, angle, dihedral allow calculation of virtual bonds, etc based on
the center of mass of the atom selection. For example if you want the
distance between the center of masses of two residues :1 and :2 you would

distance d1 :1 :2 out d1.dat

For your dihedral evaluation, you would write

dihedral zx .H64 @C29 @C30 @H66 out ph2

I will alter the output to be more specific and try to update the manual
to be clearer.

Good luck,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
| e-mail: phone: (801) 587-9652 FAX: (801) 585-9119
\ Offices: BPRP295A / INSCC 418

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Received on Thu Jul 24 2003 - 17:53:01 PDT
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