[AMBER] Antechamber error in creating FF for charged organic molecule

From: Giulia Sormani via AMBER <amber.ambermd.org>
Date: Wed, 15 Jun 2022 12:40:03 +0200

Good morning to everyone,

I am trying to built the force field to simulate an organic molecule (DFO)
which has a charge of -2.
I am using the following command:
antechamber -i DFO_2minus.pdb -fi pdb -o DFO.mol -fo mol2 -c bcc -s 2 -nc -2

However I get the following error:
 Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time

Total number of electrons: 304; net charge: -2

/cineca/prod/opt/applications/amber/16.0/intelmpi--2017--binary/bin/sqm -O
-i sqm.in -o sqm.out
Error: cannot run
-O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
I read from previous mails that when you get this warning probably there
actually is a problem with the input file.
I am sure the connectivity of the molecule is fine, I don't see where is
the problem.
I put in the attachment the input file, could someone help me with this?

Giulia Sormani

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Received on Thu Aug 04 2022 - 13:30:38 PDT
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