AMBER Archive (2003)

Subject: AMBER: (no subject)

From: Narang Manpreet Kaur (preetdbs_at_iitr.ernet.in)
Date: Thu Jul 24 2003 - 06:57:36 CDT

 Dear Amber Users,
  I am using the ptraj program (on amber6.0)to compute the dihedrals etc
from the trajectory file containing two residues 1. drug molecule and
2.water
the script is as follows:
trajin ne2pd500.traj
 trajout ne2pd500_out.traj
 rms first out ne2pd500_rms @C,P,O
average ne2pd500 pdb
dihedral zx @H64,C29,C30,H66 ph2
go
 while caculating dihedrals it gives the following error:

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)
WARNING in ptraj(), dihedral: Error in specification of the third mask
Ignoring command

I am not able to understand this can you plese provide help. Also, is
this the right format to define the atoms or not. thanks in advance.

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

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