Re: [AMBER] Parmchk2 - Atom type of CX does not shown up in PARMCHK.DAT

From: David A Case <>
Date: Thu, 13 Oct 2016 12:11:12 -0400

On Thu, Oct 13, 2016, Miha Purg wrote:
> I was trying to use parmchk2 on a non-standard residue (see attached
> .prepin) that contains a 'CX' atom type...
> "parmchk2 -i FGly_deprot.prepin -f prepi -o FGly_deprot.frcmod -a Y -p
> $AMBERHOME/dat/leap/parm/parm10.dat"
> ...and I received the following error:
> "Atom type of CX does not shown up in PARMCHK.DAT"
> I manually changed the atom type of CA from 'CT' (obtained with antechamber
> -at amber) to 'CX' to be consistent with ff14SB. Has PARMCHK.DAT not been
> updated for ff14SB or am I missing something?

Yes: the antechamber notion of "amber atom type" has not been updated. The
specific problem of changes in FF14SB can be addressed, and we will try to do
that. The more general problem is tougher: what constitutes an "Amber atom
type" is very much a moving and variable target. Both the nucleic acid
community (e.g. bsc1) and the protein people (e.g. in ff15ipq) are adding
atoms types right and left.

The parmchk2 program was primarily designed to estimate force constants
for gaff and gaff2 atom types, which are under antechamber's control. You
can (try to) use the program with Amber atom types, but you should be
triply careful to check the most cases, it will be better
to do this job by hand. Note *especially*: if your modified residue has
chemical functionality that is different from that in the standard amino
acids and nucleotides supported by Amber atom types, then Amber atoms
types are not the appropriate universe to be working in.

[cc-ing this Junmei. I'm wondering if we should really be trying to
support the "-p" option in parmchk2. Maybe we could expand the options
for the "-s" flag to a restricted set of Amber parameter files, and not
try to allow an arbitrary file to be read in via the "-p" option.]

Thanks for the report.


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Received on Thu Oct 13 2016 - 09:30:02 PDT
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