Dear Amber users
Hi
I am working on peptide from pdb and I had my ligand (aromatic organic molecule, for which I created the topology and coordinate file using GAFF). My goal is to get the complex of the peptide and my ligand and run molecular dynamic simulation on the complex. I docked my ligand to my peptide and to create the topology and coordinate file for the complex I tried to use GAFF and I got the following error. Would please please help me in figure out what is wrong with my approach to my problem? Can you please tell me a step I should follow if mine is wrong? Thank you very much in advance.
antechamber -i solution.pdb -fi pdb -o solution.prepin -fo prepi -c bcc -s2
The atom number exceeds the MAXATOM, reallocate memory
Info: the bond number exceeds MAXBOND, reallocate memory automatically
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
For atom[82]:O, the best APS is not zero, exit
For atom[87]:N, the best APS is not zero, exit
For atom[391]:N, the best APS is not zero, exit
For atom[804]:O24, the best APS is not zero, exit
For atom[805]:O25, the best APS is not zero, exit
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 MAXVASTATE in define.h and recompile bondtype.C
(4) increase PSCUTOFF in define.h and recompile bondtype.C
Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer time
Error: cannot run "/home/wberhanu/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of antechamber.c properly, exit
With best regards
Workalemahu
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Received on Sun May 31 2009 - 01:08:17 PDT
