[Chimera-users] Error in generating sqm for FAD

[Eric Pettersen]

Hi Isha,
	I have no problem charging the FAD, though it takes quite a long time to finish and I'm sure the protonation in my trial differs from yours, since the net charge for me is -2 whereas for you it is +1 (not +5; I don't know why you think it was +5 but the "-nc 1" part of the antechamber command you sent indicates a net charge of +1).
	The first problem is that the structure you sent is protonated wrong in two ways.  First, in your structure only non-carbon atoms are protonated.  Charge determination requires all protons be present.  Second, in your structure the oxygens of the flavin quinone ring are protonated and they should not be.
	Correcting these problems can be done in a few steps.  First, open the Chimera command line (Favorites->Command Line) and type "del H".  This will delete all the hydrogens.  Now we need to tell Chimera that the quinone oxygens are ketones, not alcohols.  To do this select the two oxygens and then type "setattr a idatmType O2 sel" (i.e. the atom type of the selected atoms is sp2 oxygen).  Then we need to tell chimera that the nitrogen between the those two should be protonated.  Do this by selecting that nitrogen and typing "setattr a idatmType Npl sel".
	Now add hydrogens by typing "addh".  You'll notice that the other nitrogen in the ring also gets protonated.  This is because Chimera favors a protonation state where the central flavin ring is positively charged and aromatic (i.e. a positively charged semiquinone).  To force the "classic" flavin protonation, select the extra proton and type "del sel".
	Now you will be able to run add charge.  Let me know if you have any further problems.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jan 1, 2014, at 11:08 PM, Isha <isha1520 at imtech.res.in> wrote:

> Dear Sir/Mam
> 
>  I used antechamber in chimera to add charges to ligand "FAD" using am-bcc, amber ffo3r.1 and +5 charge (as depicted by chimera). The procedure was Tools > structure editing > add H and then add charge. The error shown is :
> 
> 
> Charge model: AMBER ff03.r1
> Assigning partial charges to residue FAD (net charge +1) with am1-bcc method
> Running ANTECHAMBER command: C:/Program Files/Chimera 1.8.1/bin/amber12/bin\antechamber -ek qm_theory='AM1', -i c:\users\amehta\appdata\local\temp\tmpjjpoaq\ante.in.mol2 -fi mol2 -o c:\users\amehta\appdata\local\temp\tmpjjpoaq\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2
> (FAD)
> 
> (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> 
> (FAD)
> 
> (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> 
> (FAD) Total number of electrons: 412; net charge: 1
> 
> (FAD)
> 
> (FAD) Running: "C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out
> 
> (FAD) Error: cannot run ""C:/Program Files/Chimera 1.8.1/bin/amber12/bin/sqm" -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
> 
> Failure running ANTECHAMBER for residue FAD
> 
> 
> Please help as it is very urgent. Hope for your reply. I have also attached the ligand. Please find the attachment.
> 
>  
> With Regards,
> Isha
> C/O Dr. Raman Parkesh
> Protein Science & Engg.
> Institute of Microbial Technology
> Sector 39A, Chandigarh 160036
> Ext: 0172-6665489
> <DE_fad.pdb>_______________________________________________
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