[Dock-fans] AM1-BCC

Gustavo HMF Souza desouz at fcm.unicamp.br
Wed Oct 4 10:26:22 PDT 2006


Hi all,

1 - What´s the difference between AM1-BCC and Gasteiger in Antechamber?
Which one of them is suitable for peptides for example?

 

2- How can I add hydrogens and run antechamber using bash (without Chimera)
and 

 

It appears to be an error when I input a ligand (with previously added
hydrogens) with more than 7 aminoacids. See errors above:

 

“ms

finished 1 of 15 atoms

position #0:1.het at CG2 away from #0:1.het at CG1 [1.71]

position #0:1.het at CEI away from #0:1.het at CEH [1.70]

position #0:1.het at CEH away from #0:1.het at HEF [1.58]

position #0:1.het at CAZ away from #0:1.het at HBI [1.24]

position #0:1.het at CBA away from #0:1.het at NAX [1.66]

position #0:1.het at CCZ away from #0:1.het at 1HBQ [1.29]

position #0:1.het at ODU away from #0:1.het at HEG [1.49]

position #0:1.het at NEN away from #0:1.het at CEQ [1.74]

position #0:1.het at CCR away from #0:1.het at NCO [1.68]

position #0:1.het at OBK away from #0:1.het at NCD [0.87]

position #0:1.het at CCQ away from #0:1.het at HCW [1.53]

position #0:1.het at CG1 away from #0:1.het at N [1.63]

position #0:1.het at CCY away from #0:1.het at NBN [1.39]

position #0:1.het at NBN away from #0:1.het at 3HCZ [1.24]

finished 15 of 15 atoms

Running ANTECHAMBER command:
/usr/local/chimera/bin/antechamber/exe/antechamber -i
/tmp/tmp-e02bY/ante.in.mol2 -fi mol2 -o /tmp/tmp-e02bY/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2

(DRG) Running: "/usr/local/chimera/bin/antechamber"/exe/bondtype -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j part

(DRG) 

(DRG) Info: the atom number exceeds the MAXATOM, reallocate memory
automatically

(DRG) Running: "/usr/local/chimera/bin/antechamber"/exe/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

(DRG) 

(DRG) Info: the atom number exceeds the MAXATOM, reallocate memory
automatically

(DRG) Total number of electrons: 985; net charge: -1

(DRG) Number of electrons is odd: 985

(DRG) Please check the total charge and your -nc flag

(DRG) 

(DRG) The atom number exceeds the MAXATOM, reallocate memoryFailure running
ANTECHAMBER for residue DRG”

 

 

How can we get round this? (This occurs only when I select AM1-BCC
calculation).!

 

Best regards for all,

Gustavo Souza,

UNICAMP 

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