Dear Amber community,
I would like to correct some ligand protonation using the reduce command.
However, my ligand (5QM) is not in the
$AMBERHOME/dat/reduce_wwPDB_het_dict.txt file, so reduce cannot process it.
I checked the Chemical Component Dictionary
(
ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif), my ligand
topology is actually defined there.
The two files differ by their format, so I cannot just copy the missing
ligand record into the $AMBERHOME/dat/reduce_wwPDB_het_dict.txt file.
I would like to add my missing ligand by either:
- convert the Chemical Component Dictionary file in a format
readable by reduce
- update the $AMBERHOME/dat/reduce_wwPDB_het_dict.txt file
Any suggestion?
Second option might be tricky for me as I work behind a proxy.
Thank you in advance for your replies and have a great day.
Best regards,
Jose Manuel
--
José-Manuel Gally
/PhD Student
Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA)
UMR CNRS-Université d'Orléans 7311
Rue de Chartres
F-45067 Orléans
phone: +33 238 494 577/
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Received on Thu Jun 30 2016 - 01:00:03 PDT
