Re: [AMBER] topology file, segment id and the pathways plugin

From: Jason Swails <>
Date: Tue, 17 Mar 2015 16:54:18 -0400

On Tue, Mar 17, 2015 at 4:33 PM, Shoresh Shafei <>

> Hi,
> I ran NAMD simulations for molecules prepared by AMBER force fields and
> then used the results (trajectory and topology file) in the pathways plugin
> in VMD to find the strongest pathways between the donor and acceptor. When
> running the plugin, we get this error: cannot parse selection text: segid
> {} and resid BLAH and name BLAH, where BLAH could be anything!! I have
> narrowed down the issue with a colleague of mine to segment id assignment
> in the topology file. It looks like that, in the generated topology file
> using amber, the segment ID is not getting set for the molecule we are
> working with. The question is: how can I make sure that the the segment id
> is set in the topology file?

‚ÄčThe segment ID is a CHARMM thing. Amber topology files do not have any
notion of what a SEGID is (it looks an awful lot like a 'chain ID' to me,
but Amber prmtops don't store those by default, either).

If the segid is part of the selection string you are inputting, you will
need to find an alternate way to specify the same selection without using
segid. If that is hard-coded in the path finder tool directly, you will
either need to change the relevant source code to avoid referencing SEGID
or go through the CHARMM or VMD autopsf setup route instead.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 17 2015 - 14:00:04 PDT
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