Hi,
I'm using ambertools 13 and I have a solvated (TIP4P) trajectory and the
topology files used to create it.
I created an average pdb structure of just the protein atoms. i.e. no
solvent or ions, then I added waters from the original solvated trajectory
to the end of the pdb using cat. As I would like to rms fit the protein in
the trajectory and output pdbs with protein and water molecules only. I
tried:
#############################
parm jo_solv.parm [full]
trajin traj1.crd 1 1 1 [full]
autoimage
strip :K+
parm jo_solv_noIons.parm [noIons]
reference jo_proteinOnly.pdb [noIons] [fit]
rmsd fakefit :1-89.N,CA,C ref [fit] :1-159.N,CA,C mass out testFit.dat
trajout Jo_noIons.pdb PDB multi nobox
EOF
#################################
I don't think this is the correct way to do it and I get the following
error:
"Warning: Could not determine atomic number from name [EPW ]"
Could anyone please help me as to the correct way to do this?
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Received on Tue Jun 30 2015 - 13:00:02 PDT
