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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Received on Fri Sep 09 2005 - 21:53:01 PDT
