[Chimera-users] [Dock-fans] How to get the charged mol for the ligand

cpsosa at comcast.net cpsosa at comcast.net
Mon Feb 4 12:02:30 PST 2008


Thanks.  We tried that but after the hydrogens were added.  We saved it and "vi" the mol2 file.  I'll try this.

--
Carlos P. Sosa

 -------------- Original message ----------------------
From: Eric Pettersen <pett at cgl.ucsf.edu>
> I forgot, there's actually a fourth thing you can do:  change the  
> atom type directly.  Select the oxygen atom and open the command line  
> (Favorites->Command Line) and type:
> 
> 	setattr a idatmType O3 sel
> 
> which will set the selected atom's "idatmType" attribute to sp3  
> oxygen ("O3").
> 
> Do this before hydrogens are added.
> 
> --Eric
> 
>                          Eric Pettersen
>                          UCSF Computer Graphics Lab
>                          http://www.cgl.ucsf.edu
> 
> 
> On Feb 3, 2008, at 1:27 PM, Eric Pettersen wrote:
> 
> > Hi Carlos,
> > 	There are basically three things you can do:
> >
> > 1) Download the latest daily build and try that.  I have been  
> > working hard on atom typing for ring systems recently (and am still  
> > working on it) and there's a pretty good chance that it will type  
> > (and therefore protonate)  the phenyl oxygen correctly now.  You  
> > get a daily build by going to the Chimera home page  
> > (www.cgl.ucsf.edu/chimera) and following the "Daily Builds" link.
> >
> > 2) Directly edit the structure (after adding hydrogens but before  
> > adding charges).  Control-double-click the oxygen and select  
> > "Modify Atom" from the pop-up menu.  In the resulting dialog change  
> > the element type to O, the geometry to tetrahedral, and the number  
> > of bonds to 2.  You should also probably change the atom name field  
> > to be the same as what the atom's name is.  Then click the Change  
> > button and the hydrogen will be added.
> >
> > 3) Before doing any processing, change the bond length.  Control  
> > double-click on the C-O bond and choose "Set Bond Length" from the  
> > pop-up menu.  Type in a bond length appropriate for a C-O single  
> > bond and then run the rest of your processing.
> >
> > --Eric
> >
> > 	Eric Pettersen
> > 	UCSF Computer Graphics Lab
> >
> > On Feb 2, 2008, at 5:19 PM, cpsosa at comcast.net wrote:
> >
> >>
> >> Hello,
> >>
> >> We have the opposite problem, our PDB has one oxygen that is part  
> >> of a phenyl group and after using addH in Chimera, hydrogen does  
> >> not get added to that oxygen.  Is there a way to add hydrogen to a  
> >> single atom?  using Chimera.  For Chimera to add a hydrogen to  
> >> that O... perhaps making the C-O bond larger.
> >>
> >> Any suggestions?
> >>
> >> Thanks,
> >>
> >> --
> >> Carlos P. Sosa
> >>
> >>  -------------- Original message ----------------------
> >> From: Eric Pettersen <pett at cgl.ucsf.edu>
> >>> I assume this is IMZ from 1rv1?  Chimera is adding a proton to  
> >>> the N3
> >>> nitrogen that it shouldn't.  After adding hydrogens and before  
> >>> saying
> >>> OK to the charge calculation, type this command to Chimera's command
> >>> line to delete the extra hydrogen:
> >>>
> >>> del :IMZ at h3
> >>>
> >>> --Eric
> >>>
> >>>                          Eric Pettersen
> >>>                          UCSF Computer Graphics Lab
> >>>                          http://www.cgl.ucsf.edu
> >>>
> >>>
> >>>> I could not get the charges for my molecule (ligand in x-crystal
> >>>> structure). how to do that?
> >>>>   I am getting the following error message.
> >>>>   I am using chimera to do these funtions.
> >>>>
> >>>>   Running ANTECHAMBER command: C:\Program Files\Chimera\bin
> >>>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp
> >>>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 
> >>>> \temp
> >>>> \tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2
> >>>> (IMZ)
> >>>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe
> >>>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o  
> >>>> ANTECHAMBER_BOND_TYPE.AC -
> >>>> f ac -j part
> >>>> (IMZ)
> >>>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe
> >>>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> >>>> (IMZ) Total number of electrons: 351; net charge: 1
> >>>> (IMZ) INFO: Number of electrons is odd: 351
> >>>> (IMZ)       Please check the total charge (-nc flag) and spin
> >>>> multiplicity (-m flag)
> >>>> Failure running ANTECHAMBER for residue IMZ
> >>>>
> >>>>
> >>>>   Thomas
> >>>
> >>>
> >>
> >>
> >>
> >> From: Eric Pettersen <pett at cgl.ucsf.edu>
> >> Date: January 31, 2008 12:54:24 PM PST
> >> To: dock-fans at docking.org
> >> Subject: Re: [Dock-fans] How to get the charged mol for the ligand
> >>
> >>
> >> I assume this is IMZ from 1rv1?  Chimera is adding a proton to the  
> >> N3 nitrogen that it shouldn't.  After adding hydrogens and before  
> >> saying OK to the charge calculation, type this command to  
> >> Chimera's command line to delete the extra hydrogen:
> >>
> >> del :IMZ at h3
> >>
> >> --Eric
> >>
> >>                         Eric Pettersen
> >>                         UCSF Computer Graphics Lab
> >>                         http://www.cgl.ucsf.edu
> >>
> >>
> >>> I could not get the charges for my molecule (ligand in x-crystal  
> >>> structure). how to do that?
> >>>   I am getting the following error message.
> >>>   I am using chimera to do these funtions.
> >>>
> >>>   Running ANTECHAMBER command: C:\Program Files\Chimera\bin 
> >>> \antechamber\exe\antechamber -i c:\docume~1\thomas\locals~1\temp 
> >>> \tmpkzw4il\ante.in.mol2 -fi mol2 -o c:\docume~1\thomas\locals~1 
> >>> \temp\tmpkzw4il\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2
> >>> (IMZ)
> >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe 
> >>> \bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o  
> >>> ANTECHAMBER_BOND_TYPE.AC -f ac -j part
> >>> (IMZ)
> >>> (IMZ) Running: "C:\Program Files\Chimera\bin\antechamber"\exe 
> >>> \atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> >>> (IMZ) Total number of electrons: 351; net charge: 1
> >>> (IMZ) INFO: Number of electrons is odd: 351
> >>> (IMZ)       Please check the total charge (-nc flag) and spin  
> >>> multiplicity (-m flag)
> >>> Failure running ANTECHAMBER for residue IMZ
> >>>
> >>>
> >>>   Thomas
> >>
> >>
> >> _______________________________________________
> >> Dock-fans mailing list
> >> Dock-fans at docking.org
> >> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >>
> >>
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 


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Subject: Re: [Chimera-users] [Dock-fans] How to get the charged mol for the
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