Through out the CONECT records in the PDB and try again. I
would also guess that S-adenosyl methionine has been subject to previous
studies so you may find parameters in the literature or in a database
like R.E.D. (?).
On Mon, 2 Mar 2015 15:51:07 +0530
Swithin Hanosh <swithinhanosh.gmail.com> wrote:
> Dear Amber users ,
>
> 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
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>
> 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 sqm.in -o sqm.out
>
> Running: /home/damp/amber14/amber14/bin/am1bcc -i
> ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
> /home/damp/amber14/amber14/dat/antechamber/BCCPARM.DAT -s 2 -j 1
>
> Running: /home/damp/amber14/amber14/bin/atomtype -f ac -p bcc -o
> ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
>
>
> The outputs generated are attached with the mail. Please explain what
> may be the possible cause of error.
>
>
> Thank You,
> Swithin Hanosh
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Received on Mon Mar 02 2015 - 02:30:03 PST
