Re: [AMBER] strange tleap error with bond command

From: David A Case <>
Date: Sun, 13 Jun 2021 21:37:14 -0400

On Sat, Jun 12, 2021, Vaibhav Dixit wrote:

>I'm getting the following unexpected error with bond command.

Unfortunately, you don't show anything about bond commands you may have
given to tleap.

>The problem is with connecting residue 86 with residue 87 (named HD1).
>The desc commands below shows that C and N of these residues are not
>connected initially, thus I don't understand why I'm getting this error
>trying to connect these residues.

The small part of the output you provide doesn't establish that the error is
related to "trying to connect these residues". It might be, but it might be
from something else.
>The parmtop, inpcrd file get created if I avoid connecting 86 to 87....

This is good information, but is no real substitute for allowing someone on
the list to try to reproduce the error. It's likely, (whether or not the
error is somehow in the input or whether it is a true bug in the code) that
there is some odd interaction between different things you are doing. So
trying to create a simple example that illustrates the error. And the
process of trying to make such an example often itself leads to finding the

>!FATAL: Message: 1-4: cannot add bond 3598 3600
>This may be caused by duplicate bond specifications;
>for example, explicit bond commands in addition to PDB conect records.

Just to be sure: are atoms 3598 and 3600 the ones that connect residues
86 and 87? And are there any CONECT records in the PDB file?


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Received on Sun Jun 13 2021 - 19:00:02 PDT
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