Dear Amber Users
I am using antechamber for one residu of a polymer containing 65 atoms.
When I do this command
$AMBERHOME/exe/antechamber -i cen.pdb -fi pdb -o cen.prepin -fo prepi -c bcc -s
2 -nc 0
I get this error message:
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 MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
Be cautious, use a large value of PSCUTOFF (>10) will significantly increase
the computer time
Error: cannot run "/opt/software/SGI/AMBER/amber9/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
judgebondtype() of antechamber.c properly, exit
When I change bcc to gas I get the same error.
I added -c bcc -j 5
$AMBERHOME/exe/antechamber -i cen.pdb -fi pdb -o cen.prepin -fo prepi -c bcc -s
2 -j 5 -nc 0
I get another error message:
otal number of electrons: 274; net charge: 0
Running: $AMBERHOME/exe/divcon
/opt/software/SGI/intel/mkl/10.0.3.020/lib/em64t/libmkl_mc.so: undefined symbol:
mkl_blas_xddot
Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly, exit
Antechamber only works for -c gas -j 5
I really do not understand why is this happening, all elements are O, N, C, and
H.
Later, using the prepin file, I used parmchk
$AMBERHOME/exe/parmchk -i cen.prepin -f prepi -o cen.frcmod -a Y
’-a Y’ : this is to prints out all
force field parameters used by the input molecule, but instead i get only few
angles for the missing ff parameters in leaprc.gaff.
Is my command wrong? (-a Y)
thanks for any comments on these matters.
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Received on Mon Aug 02 2010 - 12:00:10 PDT
