Hello,
I am unable to open a pdb file in molmol, the error message is
unknown residues: DA, DC, DG, DT, HIE, Na+
unknown atoms: OXT (ARG+), OXT (GLU), H1, H2, H3 (LYS+), H1, H2, H3 (MET)
I started with a pdb file from the protein data bank, i ran a
minimization and then i used ambpdb to create a pdb file from *.rst
file. I would like to compare the initial pdb file to the pdb file after
minimization
> ambpdb -p *.prmtop < *.rst> *.pdb
i tried -aatm option and protonate -d $AMBERHOME/dat/PROTON_INFO.Brook
-i old.pdb new.pdb
is there another way to create a pdb file?
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Received on Fri Dec 05 2008 - 18:39:22 PST
