Re: [AMBER] topology problems

From: David A Case <>
Date: Wed, 8 Apr 2020 07:37:08 -0400

On Tue, Apr 07, 2020, Seibold, Steve Allan wrote:

>Since the prmtop
>file does not call for a OXT at that position, how is ambpdb creating it?

It's not. I can't see any way that ambpdb would add an OXT if it is not
there in the prmtop file. Did you open the prmtop file in a text editor
to see what atoms are actually there?


p.s. Matias has a very good guess: if your chain ID's were different,
that would cause tleap to insert a break. It would also be worth
knowing what version of AmberTools you are using, since older versions
operated differently with regard to TER cards. (But no version ever
added new OXT atoms....)

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Received on Wed Apr 08 2020 - 05:00:01 PDT
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