Re: [AMBER] parmchk vs parmchk2

From: <>
Date: Fri, 5 Aug 2016 01:08:21 +0000

Hi David,

Many thanks for your advice. It ran successfully this time!

Thought I should let you know - I had taken the parmchk -s gaff2 advice from the post here: It might be worth adding a footnote or comment about the -s 2 being the correct parmchk2 flag.

Cheers and thanks,


On Wed, Aug 03, 2016, wrote:
> I am using AMBER16 and have successfully parameterised a 4-membered
> calixarene with gaff2 using antechamber, however I get the error "Atom
> type 1 does not show up in PARMCHK.DAT" when I try to run parmchk2 (both
> with and without the -s gaff2 flag).

1. you should run "parmchk2 -s 2 ...." after an antechamber run with
the "-at gaff2" flag. Don't use "parmchk2 -s gaff2", and don't use the
outdated parmchk program. (It would be good to make the command line flags
for antechamber and parmchk2 more consistent.)

2. If this doesn't solve the problem, please post the pdb file you used
as input for antechamber. The gaff2 force field is still new, and there
may well be corner cases (pun intended) that are not well handled. You might
want to see what you get with "antechamber -at gaff".

3. Generally, no one should use parmchk any more, although it might still
work. I'm thinking of removing it from the amber16/bin directory; this
would break some workflows (which is why this has not been done before now),
but the danger of people using the wrong program probably outweighs the
inconvenience of not having it around. Comments welcome.


Many thanks, David.

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Received on Thu Aug 04 2016 - 18:30:02 PDT
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