Dear all,
We solved the issue by using resp charges generated with antechamber and
g16 output file.
I hope that this helps someone on the list in the future while dealing with
molecules with multiple fused rings.
Thank you and best regards.
On Thu, Mar 3, 2022, 17:01 Vaibhav Dixit <vaibhavadixit.gmail.com> wrote:
> Dear All,
> We are preparing a ligand for MD simulation, but getting the following
> error for which the available solutions are not relevant (since I don't
> have connectivity in the PDB given to tleap).
> Can you please suggest what might be the source of this error?
> I have attached the pdb, mol2 and frcmod files and tleap script that are
> giving the error.
> Looking forward to valuable suggestions from the list.
> Thank you and best regards.
>
> /home/niperg/Downloads/amber20/bin/teLeap: Warning!
> The unperturbed charge of the unit (1.001998) is not zero.
>
> /home/niperg/Downloads/amber20/bin/teLeap: Note.
> Ignoring the warning from Unit Checking.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> !FATAL ERROR----------------------------------------
> !FATAL: In file
> [/home/niperg/Downloads/amber20_src/AmberTools/src/leap/src/leap/unitio.c],
> line 1803
> !FATAL: Message: 1-4: cannot add bond 1 2
> This may be caused by duplicate bond specifications;
> for example, explicit bond commands in addition to PDB conect records.
> !
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Asst. Prof., Department of Medicinal Chemistry,
>
> National Institute of Pharmaceutical Education and Research, Guwahati
> (NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
> 781101, Assam, India
>
> Mob. No. +91-7709129400,
> Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
> https://niperguwahati.ac.in/DOC/profile/dixit.pdf
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> NCBI bibliography:
> https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> Please consider the environment before printing this e-mail
>
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Received on Fri Mar 04 2022 - 07:30:02 PST
