Re: AMBER: (no subject)

From: Narang Manpreet Kaur <preetdbs.iitr.ernet.in>
Date: Fri, 25 Jul 2003 09:36:54 +0500 (GMT)

  Respected Sir,
Thanks for the reply. Further I wanted to know if I want tio calculaate
more than do i have to specify one by one.

Manpreet Kaur Narang
Research Scholar
Deptt.Biotechnology
Indian Institute of Technology Roorkee (IITR)
Roorkee, 247 667 India

On Thu, 24 Jul 2003, Thomas E. Cheatham, III wrote:

>
> > > 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
> do
>
> 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: tec3.utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
> \ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418
>
>
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Received on Fri Jul 25 2003 - 05:53:01 PDT
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