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

From: Erdem Yeler via AMBER <amber.ambermd.org>
Date: Wed, 15 Jun 2022 17:58:18 +0300

Actually this answer helped me a lot, even if I was not the person who
asked this question. Thank you so much Dear David Case.
Regards,
Erdem

David A Case via AMBER <amber.ambermd.org>, 15 Haz 2022 Çar, 16:54
tarihinde şunu yazdı:

> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:31:07 PDT
Custom Search