[AMBER] antechamber error

From: Atila Petrosian <atila.petrosian.gmail.com>
Date: Thu, 17 Sep 2015 18:21:03 +0430

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
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