Re: [AMBER] no bonds formed between AA and non-standard residue

From: David A Case <>
Date: Mon, 17 Feb 2020 07:38:01 -0500

On Mon, Feb 17, 2020, Vaibhav Dixit wrote:

>Even after combine option followed by bond commands, the expected bonds are
>not generated as seen in vmd.

First: use parmed to check for bonds: then it's easy to report exactly
what you did to the list.

Second: double check that there were no errors from tleap arising from
the bond commands.

Then: post as simple an example as you can, show exactly what bond
command(s) you used in tleap, and what commands and results you got from
parmed when you interrogated the resulting prmtop file.


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Received on Mon Feb 17 2020 - 05:00:01 PST
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