AMBER Archive (2003)

Subject: ptraj rdf help

From: tianxiao yang (yang.984_at_osu.edu)
Date: Wed May 21 2003 - 17:28:26 CDT

Dear Prof.Case,

My MD system is one metal ion solvated in water. I have a big problem
running ptraj to draw RDF between solute central metal and WAT. Could you
please kindly help me out? I greatly appreciate your kind help.

My ptraj script file is:
trajin md02.mdcrd
center
radial cm-o-md00 0.05 8.5 :WAT_at_O :1_at_CM closest density 0.033456
radial cm-h-md00 0.1 8.5 :WAT_at_H2 :1_at_CM closest density 0.033456
go

The error messages are:

Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of @type)...
Read in residue labels...
  M9C WAT WAT WAT WAT WAT WAT WAT WAT WAT
  WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
  ...
  WAT WAT WAT WAT
Read in the residue to atom pointer list...
Read in bond parameters RK and REQ...
Read in angle parameters TK and TEQ...
Read in dihedral parameters PK, PN and PHASE...
Read in SOLTY...
Read in L-J parameters CN1 and CN2...
Read in info for bonds w/ hydrogen...
Read in info for bonds w/out hydrogen...
Read in info for angles w/ hydrogen...
Read in info for angles w/out hydrogen...
Read in info for dihedrals w/ hydrogen...
Read in info for dihedrals w/out hydrogen...

ERROR in readParm: ...failed to find EXCLUDED_ATOMS_LIST

Tianxiao Yang, Department of Chemistry,
The Ohio State University