Re: [AMBER] strange tleap error with bond command

From: Vaibhav Dixit <>
Date: Mon, 14 Jun 2021 10:31:25 +0530

Dear David,
I have shared all the details and files in a separate email.
Please see if you can reproduce the error and help me out in fixing the
I will post the solution here once we have figured it out.
Thanks a lot for your help and support. Best regards.

On Mon, Jun 14, 2021 at 7:07 AM David A Case <> wrote:

> 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
> problem....
> >!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?
> ...thx...dac
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Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Sun Jun 13 2021 - 22:30:02 PDT
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