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
problem.
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 <david.case.rutgers.edu> 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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--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Sun Jun 13 2021 - 22:30:02 PDT
