On Sat, Apr 04, 2015, Ziheng Wang wrote:
>
> I have been following tutorial B4, the protein-ligand system with
> sustiva. I tried to reduce the sustiva pdb file by using reduce
> sustiva > sustiva_h.pdb. However, the terminal log and the produced
> sustiva_h.pdb show that no hydrogens are added, as a result, the new
> sustiva_h.pdb has an odd number of electrons and cannot be processed by
> sqm. I wonder what caused the problem with the reduce method and how to
> fix it.
Can you post the reduce output? I suspect that it is not finding
$AMBERHOME/dat/reduce_wwPDB_het_dict.txt. This could be because your
$AMBERHOME variable is not correctly set, or because this file is not actually
present.
Or, it could be some other problem....dac
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Received on Sun Apr 05 2015 - 04:30:02 PDT
