[Chimera-users] Charges for PTR+DT

[Elaine Meng]

Hello,
Generally you should know what is in your structure. You should look at the structure and the information at the RCSB PDB and/or the paper describing the structure.  For example, when I use commands:

open 1k4t
~nuc
show :PTR,DT,TGP
rlabel :PTR,DT,TGP

I can see it is both protein and DNA.  For docking, did you really want both protein and DNA?  If you wanted the protein only, you would need to delete the DNA chains.  You might also want to delete ligand residues topotecan and others (listed at the RCSB PDB website 

To hide ribbon:sc 5
~ribbon

I already know that of the three residue types you mention, DT is usually a standard DNA residue but the others are not.  I can see that TGP is in the DNA so it must be a modified base, and that PTR is in the protein ribbon like an amino acid, but it is covalently bonded to one of the DT residues in the DNA chain.  Thus Chimera recognizes the nonstandard (PTR+DT) as a single covalently bonded unit, and both that and the TGP are nonstandard groups that require charge calculations.  The other DTs are not modified so they can just get the standard residue lookup charges.

If your question is why +2 and 0, that is simply an estimate of net charge from looking at the functional groups in these sets of atoms.  If you disagree with those values, you could change them before running the calculation.  However, usually the estimates are pretty good.

To see chemical diagrams of these nonstandard residues, use the RCSB PDB website:
<http://www.rcsb.org/pdb/explore/explore.do?structureId=1k4t>

Unlike the diagram, I see that the TGP in the structure 1k4t does not include a phosphate, so the estimate of 0 makes sense.  The combined PTR 723.A and DT 10.B is selected below, looks like it includes two phosphates with estimate of -1 for each, totaling -2.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 17, 2015, at 8:51 AM, Amali Guruge <amaligg2010 at gmail.com> wrote:
> 
> Dear all,
> 
> I have to prepare the pdb structure 1K4T to my study. When I do the dock prep process, it gives net charges as,
> PTR+DT -2
> TGP +0
> 
> I added charges for standard resides by AMBER ff12SB. For other residues, I added charges by Gasteiger method.
> 
> My problem is why PTR+DT gives -2 charge? I am not familiar with this one. 
> 
> Can anyone help me?
> 
> Thank you.

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