AMBER Archive (2005)

Subject: AMBER: AMBBER: ptraj question

From: Douali, Latifa (latifa.douali_at_pnl.gov)
Date: Fri Sep 09 2005 - 15:49:24 CDT


Hello amber users,

I ran some TI calculations and I would like to use ptraj now to
calculate the RMSd.
Here is my trajin:

trajin DGAP_md17.mdcrd
trajin DGAP_md27.mdcrd
strip :WAT

rms first out DGAP_lambda7.rms time 1

Here is a part of what I got:

Amber8 Module: ptraj
...
Scanning Box
Read in box information...
Scanning Perturbation info...
  *** PRMTOP does not contain parameters PERT_BOND_ATOMS
  Bonds...
  *** PRMTOP does not contain parameters PERT_BOND_PARAMS
  Angles...
  *** PRMTOP does not contain parameters PERT_ANGLE_ATOMS
  *** PRMTOP does not contain parameters PERT_ANGLE_PARAMS
  Dihedrals...
  *** PRMTOP does not contain parameters PERT_DIHEDRAL_ATOMS
  *** PRMTOP does not contain parameters PERT_DIHEDRAL_PARAMS
  Extra perturbation information...
  *** PRMTOP does not contain parameters PERT_RESIDUE_NAME
  *** PRMTOP does not contain parameters PERT_ATOM_NAME
Successfully completed readParm.

PTRAJ: Processing input file...
       Input is from standard input
     
...

I am wondring why it gives me this message even if these parameters are
in the prmtop.

Thank you very much

Latifa

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