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

From: Shoresh Shafei <shoresh.shafei.duke.edu>
Date: Tue, 17 Mar 2015 20:33:32 +0000


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?

I appreciate your comments.

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Received on Tue Mar 17 2015 - 14:00:03 PDT
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