Re: [AMBER] Error while creating force field

From: FyD <>
Date: Tue, 03 Mar 2015 10:15:25 +0100

Dear Swithin Hanosh,

You could use R.E.D. Server Dev./PyRED at to generate a
force field for this molecule.

You could use the building block approach as defined in the F-90 REDDB
project; see:

regards, Francois

> I am trying to create force field for S-adenosyl methionine (SAM). I
> am using antechamber program (AmberTools14) for the purpose. I am
> following the antechamber tutorial 4b. After using the command
> :"antechamber -i sam-in-h.pdb -fi pdb -o sam.mol2 -fo mol2 -c bcc -s
> 2" on the input file sam-in-h.pdb (attached with the mail) , I am
> getting the following error :
> Running: /home/damp/amber14/amber14/bin/bondtype -j full -i
> For atom[4]:O, the best APS is not zero, bonds involved by this atom
> are frozen
> 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
> Running: /home/damp/amber14/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0
> -o ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 210; net charge: 0
> Running: /home/damp/amber14/amber14/bin/sqm -O -i -o sqm.out
> Running: /home/damp/amber14/amber14/bin/am1bcc -i
> /home/damp/amber14/amber14/dat/antechamber/BCCPARM.DAT -s 2 -j 1
> Running: /home/damp/amber14/amber14/bin/atomtype -f ac -p bcc -o
> The outputs generated are attached with the mail. Please explain what
> may be the possible cause of error.

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Received on Tue Mar 03 2015 - 01:30:02 PST
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