[Dock-fans] AM1-BCC

Kim Branson kim.branson at gmail.com
Wed Oct 4 10:34:05 PDT 2006


On Oct 4, 2006, at 10:26 AM, Gustavo HMF Souza wrote:

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

AM1BCC is the AMI semi empirical hamiltonian with bond centred charge  
correction. Basically parameterised to fit higher order resp fitted  
charge calculations. Its probably the  upper end of good partial  
charges with out going to qm + resp fitting.,

For a peptide, you could consider kollman i,e amber charges (same as  
your protein) or gastieger might be good enough.  7 amino acids is  
very hard to dock correctly and score.  Try validation with a few  
known systems to get a feel for whats important and some parameters  
that might work for your case.

> 2- How can I add hydrogens and run antechamber using bash (without  
> Chimera) and
For your protein or ligand?

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

It looks like you have bumping protons.   Also if you want to compute  
AM1BCC charges you'll need to recompile divcon + antechamber with a  
larger maxatoms variable.

cheers

Kim

>
>
> “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
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans



More information about the Dock-fans mailing list