Dear Swithin Hanosh,
You could use R.E.D. Server Dev./PyRED at
http://q4md-forcefieldtools.org/REDServer-Development/ to generate a
force field for this molecule.
You could use the building block approach as defined in the F-90 REDDB
project; see: http://q4md-forcefieldtools.org/REDDB/projects/F-90/
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
> 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.
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Received on Tue Mar 03 2015 - 01:30:02 PST
