Hi there,
I am using Antechamber for generating my prep file using the charges from a
gaussian output file.
I want to fit it using RESP.
For all my molecules (Non aromatic) it is working fine. But for a toluene
radical it gives me the following error.
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 "/panfs/storage/sets/maupin/common/amber11/bin/bondtype -j
full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
Antechamber generated the following two files when it gave the error
ANTECHAMBER_BOND_TYPE.AC0
ANTECHAMBER_BOND_TYPE.AC
I used these two files and tried to generate the prep file.
I made the following script for doing it
bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f
ac
cp ANTECHAMBER_BOND_TYPE.AC0 ANTECHAMBER_AC.AC0
atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
cp ANTECHAMBER_AC.AC ANTECHAMBER_RESP_PRE.AC
respgen -i ANTECHAMBER_RESP_PRE.AC -o tol_r.respin1 -f resp1
respgen -i ANTECHAMBER_RESP_PRE.AC -o tol_r.respin2 -f resp2
resp -O -i tol_r.respin1 -o tol_r.respout1 -e tol_r.esp -t -qout_stage1
resp -O -i tol_r.respin1 -o tol_r.respout1 -e tol_r.esp -q qout_stage1 -t
qout_stage2
antechamber -i ANTECHAMBER_RESP_PRE.AC -fi ac -o tol_r_resp.ac -fo ac -c rc
-cf qout_stage2
prepgen -i tol_r_resp.ac -f int -o tol_CB.prep -rn "MOL" -rf molecule.res
This gave me the following error.
Unit 10 Error on OPEN: tol_r.esp
Unit 10 Error on OPEN: tol_r.esp
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 "/panfs/storage/sets/maupin/common/amber11/bin/bondtype -j
full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
Cannot open the ac input file: tol_r_resp.ac, exit
Please advise as to how I can obtain the prep file with the RESP charges
Thank you.
Vivek Bharadwaj
Graduate Student
Chemical Engg. Department
Colorado School of Mines
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Received on Fri Jun 10 2011 - 14:00:02 PDT
