From: Arjun Sharma <arjunsharma83.gmail.com>
Date: Fri, 20 Dec 2013 10:50:08 -0600

Dear amber users,

I am trying to generate mol2 file from pdb file of a polymer which is 120 atoms long but I keep bumping into this error message when I try to run antechamber

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 "/usr/local/packages/amber/10/intel-11.1-mvapich-1.1/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit

I did get mol2 files from pdb files of polymers which were 118 and 119 atoms long but not for 120 atoms. I googled the error message and came across some suggestions about changing PSCUTOFF values and MAXATOM values in define.h file in antechamber. The cluster I am using has antechamber PSCUTOFF value set to 10 and MAXATOM value set to 256.

Any suggestions ?

Thanks in advance.
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Received on Fri Dec 20 2013 - 09:00:02 PST
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