Dear AMBER users
I am using AMBER 12 with force field ff12SB. I have used the
following command to strip water molecules from "concat_2to11pdbfiles.pdb"
[ which is obtained by combining production run mdcrd files and then
converting to pdb format]
*cpptraj -i ptraj_script2to11concatPDB_stripWATER -p protein_sol.prmtop*
where, the input file"ptraj_script2to11concatPDB_stripWATER" contains the
following script:
trajin concat_2to11pdbfiles.pdb
strip :WAT
trajout concat_2to11pdbfilesSTRIPwater_sol.pdb pdb
and,
"protein_sol.prmtop" is the parameter-topology file[ which has been also
used in the production run.]
The output file "concat_2to11pdbfilesSTRIPwater_sol.pdb" does not have
water molecules , but the following messages are seen in the screen :
Warning: Valence not found for for [Na+ ], using max valence (7)
Let me help to understand what it stands for. I had used Na-atom to
neutralise in leap process.
Thanks,
Mahendra Thapa
University of Cincinnati
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 25 2012 - 13:00:02 PDT
