Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains

From: David A Case <>
Date: Tue, 31 Oct 2017 08:12:23 -0400

On Mon, Oct 30, 2017, Hai Nguyen wrote:
> the script does work as expected. The index you saw did not reflect the
> atom index.

?? Does this mean there is no problem? Did you send at17.pdb to tleap?

> PS: If you see the at17.pdb content, you can see something like
> ATOM 2354 N GLN I 298 38.581 11.502 -4.835 1.00 33.77 N
> TER 2355 GLN I 298

The ambpdb code (aka cpptraj) slightly violates the PDB practice by not
incrementing the atom number on a TER card. This is extremely convenient
since then the atom number in columns 7-11 actually *is* the Amber atom number
(starting from 1).

I'm thinking that pdb4amber should do the same thing. I think (not tested)
that this would fix the problem, and would make pdb4amber more consistent with
the rest of Amber. (I've not yet seen a case where a code makes use of the
conents of columns 7-11 on a TER card.)


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Received on Tue Oct 31 2017 - 05:30:03 PDT
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