Hi Eeveryone
I want to create topology and coordinate file using ANTECHAMBER. When
I run the below command
antechamber -i 50_N.pdb -fi pdb -o 50.mol2 -fo mol2 -c bcc -s 2
It gives the below error
---Judge bond type for Residue 1 with ID of 40 and Name of SUS ---
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
Error: cannot run "/opt/apps/amber/10/openmpi-mkl/bin/bondtype -j full
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
[mustafa.coe 1fun]$ -Judge bond type for Residue 1 with ID of 40 and
Name of SUS ---
-bash: -Judge: command not found
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
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Received on Fri Jun 23 2017 - 21:30:02 PDT
