On Tue, Jun 04, 2019, Vaibhav Dixit wrote:
>I noticed that there are (small) differences in PDB file formats between
>RCSB and AMBER.
You don't say what you mean by "AMBER". [Using ambpdb gets a PDB-format
file that follows closely the wwPDB standard. Use the "-bres" option to
get standard residue names. Residue numbers and chainID's tend to get
lost when running Amber simulations, but these can be retrieved via
add_pdb and the "-ext" option to ambpdb.]
You also don't say what differences you find, or what specific
problems LeVIew has.
>LeView 2D interaction map
The hbond command in cpptraj reports on hydrogen bonds. The "closest"
command can provide contact information between the ligand and receptor.
But, by all means, Use LeView if it suits your needs.
....dac
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Received on Tue Jun 04 2019 - 05:30:02 PDT
