Hi,
I have a question concerning the use of Antechamber. When I use the
following command:
antechamber -i 1EDG_reduce.pdb -fi pdb -o EDG.mol2 -fo mol2 -c bcc -s 2
-nc -3
I get errors:
Running: /app1/linux/amber10a/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
Info: the actual number of rings (1094) exceeds the defaut ring size (500),
reallocate memory automatically
WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
WARNING: atom type of CE1 (cd) and NE2 (nc) may be wrong
Total number of electrons: 22968; net charge: -3
I believe it is due to the HIS residue but I am not really sure. Can anyone
enlighten me on this problem and maybe suggest how to solve it? I will
greatly appreciate any help.
Regards,
Ashley
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Received on Wed Oct 24 2012 - 00:00:02 PDT
