On Thu, Jun 30, 2016, Jose Manuel Gally wrote:
>
> 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'm not sure how/when/if the Duke group will update the reduce dictionary.
Here is one workaround: extract the 5QM block from the components.cif
file into a file 5QM.ccif. Then run antechamber:
antechamber -i 5QM.ccif -fi ccif -bk "5QM" -o 5QM.mol2 -fo mol2 -c bcc
This will create a mol2 file with the protons as found in the components.cif
file; if you load this into tleap, it will add those hydrogens if they are
missing from your input PDB file.
Notes:
1. components.cif assumes that most things are neutral, which may not be what
you want: you may have to edit the 5QM.mol2 file (and re-run antechamber with
the edited file as input) to get a state appropriate for the pH conditions
that are relevant to your simulation.
2. You can just feed the entire components.cif file to antechamber (in place
of the 5QM.ccif file above), but this tends to be rather slow, since the code
processes all entries before using just the info in the 5QM datablock. Some
enterprising Amber developer could fix this by editing the mmcif.c file
in the antechamber directory.
...good luck...dac
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Received on Thu Jun 30 2016 - 05:30:05 PDT
