Hi Laura,
it looks like your input structure has an issue. The total number of
electrons comes out as odd so you are likely missing either a hydrogen or a
charge somewhere (I'd also have a look at those long bond warnings). Maybe
your B-atom is engaged in an odd bonding arrangement as boron is wont to
do? Without seeing the structure it is hard to tell, but try and visualize
it and check if you have a chemically reasonable structure with all
valences saturated.
Kind Regards,
Thomas
On Thu, Feb 16, 2023 at 3:49 AM laura zhang via AMBER <amber.ambermd.org>
wrote:
> Dear amber users,
>
> I am working on a drug molecule which has a B atom. I got the following
> error message when trying to generate forcefield parameters for this
> molecule using antechamber.
>
> -- Check Geometry --
> for those bonded
> Warning: Large distance for BOND 80 C27 F 0
> 1.54 [0.90 - 1.54]
> Warning: Large distance for BOND 81 C27 F1 0
> 1.54 [0.90 - 1.54]
> for those not bonded
> -- Check Weird Bonds --
> Status: pass
> -- Check Number of Units --
> Status: pass
> acdoctor mode has completed checking the input file.
>
> Info: Bond types are assigned for valence state (7) with penalty (1).
> Info: Total number of electrons: 393; net charge: 0
> Info: The number of electrons is odd (393).
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag).
>
> Running: /home/amber20/bin/sqm -O -i sqm.in -o sqm.out
> /home/amber20/bin/wrapped_progs/antechamber: Fatal Error!
> Cannot properly run "/home/amber20/bin/sqm -O -i sqm.in -o sqm.out".
> Cannot open file (drug_antechamber.mol2) with mode (r).
> No such file or directory
>
> I am wondering how to solve the issue. Thank you very much.
>
> Laura
>
>
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>
--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Thu Feb 16 2023 - 00:00:02 PST
