Re: [AMBER] A few issues

From: Hai Nguyen <>
Date: Thu, 14 Feb 2019 23:48:02 -0500

On Wed, Feb 13, 2019 at 10:31 AM Hai Nguyen <> wrote:

> On Wed, Feb 13, 2019 at 9:55 AM Paul, Austin <>
> wrote:
>> c.) When running pdb4amber, the -add-missing-atoms parameter does not
>> work: it appears to be sourcing an old version of the forcefield file.
>> Either the location or the name/capitalization has changed, which should
>> fix the issue.
> thanks for your report about pdb4amber. It's my mistake to not hide some
> experimental options. I will have a fix (if possible).

hi Austin,
I've tried the option with pdb4amber in AmberTools 18 and it seems fine.
Which amber version are you referring to? PS: I think I met the issue
before with error message "Could not open file leaprc.dna.bsc1: not found""
but I can't reproduce it.

$ pdb4amber missing.pdb --add-missing-atoms -o full.pdb


Summary of pdb4amber for: missing.pdb



The following (original) chains have been found:

---------- Alternate Locations (Original Residues!))

The following residues had alternate locations:


---------- Mising heavy atom(s)

ARG_2 misses 7 heavy atom(s)

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Received on Thu Feb 14 2019 - 21:00:03 PST
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