On Wed, Jun 15, 2022, Giulia Sormani via AMBER wrote:
>
>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
>
>Running:
>/cineca/prod/opt/applications/amber/16.0/intelmpi--2017--binary/bin/sqm -O
>-i sqm.in -o sqm.out
>Error: cannot run
>"/cineca/prod/opt/applications/amber/16.0/intelmpi--2017--binary/bin/sqm
>-O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
>"
First, you need to look at the sqm.out file to see what the error is.
Second, if it's not obvious what to do from the sqm.out file, and geometry
optimization seems to be the problem, turn off geometry optimization and/or
change the scf convergence options: see notes #6 and #7 on p. 302-3 of the
2022 Amber Reference Manual (available on the web site -- I don't know the
page number for Amber16).
Specifically, you might want to try adding the following flag to you
antechamber run:
-ek "qm_theory='AM1', maxcyc=0, scfconv=1.d-8, ndiis_attempts=700,"
[It's probably a good general idea to update to AmberTools22, and to start
using GAFF2. But this is unlikley to be really related to the problem you
are seeing.]
...hope this helps....dac
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Received on Thu Aug 04 2022 - 13:30:54 PDT
