[AMBER] drug including B atom

From: laura zhang via AMBER <amber.ambermd.org>
Date: Thu, 16 Feb 2023 02:49:31 +0000

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.


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Received on Wed Feb 15 2023 - 19:00:02 PST
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