[Chimera-users] Failure With DockPrep

Eric Pettersen pett at cgl.ucsf.edu
Tue Jul 10 17:19:11 PDT 2012

Hi Dylan,
	You should report bugs via the Help->Report A Bug menu item rather than send them to chimera-users.
	With that out of the way, I must say I'm a little perplexed by your report.  The antechamber failure is because the formal charge specified (+0) doesn't match the protonation state of the FAD (totals to an odd number of electrons).  Did Chimera estimate the charge as zero, or did you change that in the charge dialog?  In most cases I would expect the charge of FAD to be -1 (+1 from the isoalloxazine ring, and -2 from the phosphates), though that can vary depending on the local environment.
	And deleting the FAD and getting the same error message makes absolutely no sense to me, since Chimera doesn't even send Zn to antechamber; it simply assigns +2 as the charge to the zinc atom.
	When I open 1qr2 (a two-chain NQO2 structure) I can run DockPrep on it without error, though it does take a long time to compute the charges for the FADs.  Therefore, if the above info isn't enough for you to solve the problem you'll have to use that Report A Bug menu item and attach your structure to make further progress.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Jul 10, 2012, at 7:42 AM, Dylan J. Bennett wrote:

> Hi, I am attempting to run DockPrep on NQO2 which contains an FAD cofactor. Everything works until it attempts to add charges to FAD at which point it returns an error message. If I delete FAD it will return the same error message for the Zn ion. It seems to be unable to add charges for any non-amino acid molecules. I am running the latest stable build of Chimera. Interestingly, I know Chimera used to be able to calculate these charges with an old version I had but seems no longer able. Below is the reply log. Thank you.
> #0, chain A: nrh dehydrogenase [quinone] 2
> #0, chain B: nrh dehydrogenase [quinone] 2
> No incomplete side chains
> Terminii for WT_noH.pdb (#0) chain A determined from SEQRES records
> Terminii for WT_noH.pdb (#0) chain B determined from SEQRES records
> Chain-initial residues that are actual N terminii: ALA 1.A, ALA 1.B
> Chain-initial residues that are not actual N terminii: 
> Chain-final residues that are actual C terminii: GLN 230.A, GLN 230.B
> Chain-final residues that are not actual C terminii: 
> 482 hydrogen bonds
> Hydrogens added
> Charge model: AMBER ff99SB
> Assigning partial charges to residue ZN (net charge +2) with am1-bcc method
> Assigning partial charges to residue FAD (net charge +0) with am1-bcc method
> Running ANTECHAMBER command: C:/Program Files/Chimera 1.6.2/bin/amber11/bin\antechamber -ek qm_theory='AM1', -i c:\docume~1\dylan_~1\locals~1\temp\tmpy6za6o\ante.in.mol2 -fi mol2 -o c:\docume~1\dylan_~1\locals~1\temp\tmpy6za6o\ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
> (FAD) 
> (FAD) 
> (FAD) Total number of electrons: 407; net charge: 0
> (FAD) INFO: Number of electrons is odd: 407
> (FAD)       Please check the total charge (-nc flag) and spin multiplicity (-m flag)
> (FAD) 
> (FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/sqm" -O -i sqm.in -o sqm.out
> (FAD) Error: cannot run ""C:/Program Files/Chimera 1.6.2/bin/amber11/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
> (FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> (FAD) 
> (FAD) Running: "C:/Program Files/Chimera 1.6.2/bin/amber11/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> Failure running ANTECHAMBER for residue FAD
> Check reply log for details
> -- 
> -Dylan J. Bennett
>  Dylan.John.Bennett at Gmail.com
>  (914) 621-1149
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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