AMBER Archive (2003)

Subject: Re: AMBER: (no subject)

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu Jul 24 2003 - 10:38:15 CDT

Narang Manpreet Kaur wrote:
>
> 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)

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

Best regards

Holger

> 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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-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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