Re: [AMBER] Virtual Spin Labels in Amber

From: David Case <>
Date: Sat, 12 Jan 2019 22:00:57 +0000

On Thu, Jan 10, 2019, Kari Gaalswyk wrote:
>I am trying to incorporate a virtual spin label into a protein ...
>addAtomTypes {
>{“OND”, “ON”, “sp3”} //new atom type

This is wrong: the second string has to be an element (i.e. an entry in
the periodic table. [As a special case, it can be a blank string,
representing an "extra point"; but you can't just put somehting like
"ON" in there.

In the string above "OND" is an atom type.

>atom type OND - unknown element ON

This is just telling you what I said above: ON is not an element.

>> foo = sequence {ALA ALA ALA ONA ALA ALA}
>ERROR: Comparing atoms
>.R<ONA 4>.A<C 9>,
>.R<ONA 4>.A<CB 5>,
>.R<ONA 4>.A<HA 4>, and
>.R<ONA 4>.A<N 1>

>to atoms
>.R<ONA 4>.A<C 9>,
>.R<ONA 4>.A<CB 5>,
>.R<ONA 4>.A<OND 11>, and
>.R<ONA 4>.A<N 1>

This is odd, but there are lots of things that you have done that are
not represented here. Use the desc command to tleap to examine the
ONA residue: does it have a atom named "OND" as its 11th atom? And an
atom named "HA" as its fourth atom?

>!FATAL: In file [chirality.c], line 142
>!FATAL: Message: Atom named OND from ONA did not match !

>I get the same error if I try to load a pdb file with the modified
>residue already incorporated (both with and without the OND atom
>present). From my understanding, this is because I have defined a
>pentavalent carbon (by bonding it to the Calpha in the lib file), and the
>chirality functions are attempting to match the 4 neighbors of the CA,
>but it now has 5. Is there any way to allow for pentavalency in tleap, or
>am I going about this the wrong way? I’m not too familiar with amber’s
>inner workings.

Excellent question: chirality.c errors are often hard to follow.

Can you send your mol2 and frcmod files for the ONA residue? I think we
are going to have to be able to reproduce this problem before figuring
out what is going on.

Or, maybe someone else on the lists recognizes the "pentavalent carbon"

...good luck...dac

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Received on Sat Jan 12 2019 - 14:30:02 PST
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