Re: [AMBER] FATAL Error: Atom does not have a type (Cation)

From: David A Case <>
Date: Wed, 25 Mar 2020 22:01:11 -0400

On Wed, Mar 25, 2020, Yoanes Vianney wrote:

>ATOM 1164 K+ K+ 37 -0.900 4.645 -12.032 1.00 0.00 K
>ATOM 1165 K+ K+ 38 -2.581 2.404 -10.169 1.00 0.00 K

Created a new atom named: K+ within residue: .R<K 37>
>  Added missing heavy atom: .R<K 37>.A<K 1>
>Created a new atom named: K+ within residue: .R<K 38>
>  Added missing heavy atom: .R<K 38>.A<K 1>

PDB files are column specific. The residue name *must* be in columns
18-20. You lines above have "K+" in columns 20 and 21, so tleap
(correctly) thinks that the residue name is " K" and that there is a
"+" sign in the (otherwise unused) column 21.

Hence, tleap tells you that it thinks residue 37 is named "K": then it
sees a "K+" atom in that residue (which should not be there), and issues
the "created a new atom" message. Then, it notes that there is no "K"
atom in residue 37 (which there should be), and issues the "added
missing heavy atom" message. Same thing for residue 38.

(I recognize that this may be overkill in terms of getting things to work
for your particular problem, but learning to grok the messages
that tleap issues will really aid in understanding why things are going

....good luck....dac

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Received on Wed Mar 25 2020 - 19:30:01 PDT
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