Re: [AMBER] A few issues

From: David Case <>
Date: Thu, 14 Feb 2019 02:18:07 +0000

On Wed, Feb 13, 2019, Paul, Austin wrote:

>a.) The Amber 2018 Reference Manual makes no mention of the '-s'
>parameter that must be passed to parmchk2 in order to check against gaff2
>atom types.

Thanks: fixed for the upcoming April release.

>b.) When using tLEaP to save pdb files, the atom names are not properly
>aligned. And because atom types are not specified, other programs may
>interpret Cl-1, for example, as C-l1, treating them as carbons. I see in
>the change log that this was fixed in cpptraj a couple years ago, but
>LEaP still has the issue.

This is a harder issue. The behavior of savePdb has been around for a
long time, and we can neither remove the command (too many workflows use
it) nor easily address all the issues (although proposals for code fixes
are welcome.) I've added a warning note in the manual, pointing out the
tLeap emits "Amber" PDB files, which may not work in other applications.
I point people to the ambpdb program (based on cpptraj), which does a
much better job of meeting PDB standards.

>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.

I think Hai is addressing this issue.

...thanks for your input....regards....dac

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Received on Wed Feb 13 2019 - 18:30:02 PST
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