Re: [AMBER] ambpdb error while conversion

From: David Case <>
Date: Wed, 25 Sep 2019 12:59:07 +0000

On Tue, Sep 24, 2019, Sunita Patel wrote:

>Following that we ran the perl script to add CMAP parameter into prmtop
>file which we got from the author.
>perl ./Trans_FF_IDPs -p AH_ff14SB.prmtop -o AH_ff14SB_CMAP.prmtop -c

Two things: you may need to contact the author of the "Trans_FF_IDPs",
since this is not an Amber program. As I suggested earlier, you could
compare the output prmtop file with those in the
AMBERHOME/test/chamber/md_engine/dhfr_cmap directory. Or, post your
prmtop file so that we can try to reproduce the ambpdb problem.

If parmed is not working for you: did you accept the offer to install
miniconda when you installed AmberTools19? This is the best way to
ensure that you have all the proper modules. This version of python is
kept entirely within your AMBERHOME folder, and will not interfere with
other python installations you may have on your machine.


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Received on Wed Sep 25 2019 - 06:00:03 PDT
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