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.scripps.edu
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Received on Thu Jul 24 2003 - 16:53:00 PDT
