Before you hand the structure to antechamber you will have to make sure to have all atoms, in particular the hydrogens, added. You also need to be clear about the total charge of your molecule.
________________________________________
From: Maryam Hamzehee [maryam_h_7860.yahoo.com]
Sent: 28 January 2015 06:27
To: amber list
Subject: [AMBER] problem with antechamber
Dear Amber List
I am one of AMBER users, I am trying to do energy minimization and MD simulation for my ligand-receptor complex. I had a look to the tutorial
http://ambermd.org/tutorials/basic/tutorial4b/, but when I was doing this tutorial for my molecule, it didn't work. I generated the small molecule in hyperchem and did energy minimization and did overly of the molecule using Pymol. But the reduce and antechambercommand did not work in my system. Reduce command did not add hydrogens but generated the structure and when I ran antechamber command the following error is appeared:
[maryam.cluster catechin]$ antechamber -i catechin-over-h.pdb -fi pdb -o cat.mol2 -fo mol2 -c bcc -s 2Running: /share/apps/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 "/share/apps/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit[maryam.cluster catechin]$
I used openbabel, SPDBV, Pymol for changing the file format but none of them did work. I would be grateful if you help me in this regard.
Your reply would be highly appreciated.
All the bestMaryam
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Received on Wed Jan 28 2015 - 00:30:02 PST
