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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- application/octet-stream attachment: sqm.out
Received on Mon Mar 02 2015 - 02:30:02 PST
