Hi everybody,
I've generated an average pdb structure from a processed mdcrd file. I intend to use this average structure to generate topology files to visualise the processed trajectory.
The average structure is attached. It consists of a receptor, ligand and one water molecule (closest to the ligand).
I extracted from this average structure the ligand and save it as ligand pdb.
I then tried to generate a mol2 file by using the following command:
antechamber -i ligand.pdb -fi pdb -o bal.mol2 -fo mol2 -c bcc -s 2
I got the following 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 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 "/Users/gt/Programs/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit
I also tried the following.
Opened ligand.pdb in Chimera and save it as ligand2.pdb (This created new connectivities).
I re-run antechamber and got:
Running: /Users/tzotzos/Programs/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /Users/tzotzos/Programs/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 132; net charge: 0
Running: /Users/tzotzos/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/Users/tzotzos/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
Your help in solving this problem will be greatly appreciated.
Best regards
George
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Received on Wed May 18 2011 - 11:30:04 PDT
