Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt

From: Jose Manuel <>
Date: Sat, 2 Jul 2016 10:46:09 +0200

Dear M. Case,

thank you for your reply.

Actually, I found a script directly within the AmberTools directory that
did the trick for me:


I just replaced the $AMBERHOME/dat/reduce_wwPDB_het_dict.txt file by its
updated version.

Jose Manuel

On 30/06/2016 14:25, David A Case wrote:
> 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 Sat Jul 02 2016 - 02:00:02 PDT
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