Dear amber users,
I want to calculate binding free energy using MM-PBSA method. Based on
tutorial, I should create prmtop and inpcrd for ligand.
I obtained protein-ligand complex from docking (autodock vina). I made a
pdb file only containing ligand (lig.pdb). After using antechamber, I
encountered with following error:
$AMBERHOME/exe/antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc
-s 2
Running: /home/linux/Desktop/amber/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
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 "/home/linux/Desktop/amber/amber11/bin/bondtype -j full
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
What is the reason of this error?
How to resolve that?
Any help will highly appreciated.
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Received on Thu Sep 17 2015 - 07:00:07 PDT
