[Chimera-users] pseudobond problem while writing mol2 format

[Eric Pettersen]

Hi Kiruba,
	For each of those pseudobonds, there is a hidden “real” bond.  To have the Mol2 file treat the segments as disconnected, the hidden bonds have to be deleted.  I have attached a simple Python script that does that.  So you would open your PDB file, run the script (simply opening the .py file will run it) and then save your Mol2.
	Keep in mind that deleting those hidden bonds will change the corresponding atom types.  So for instance the backbone nitrogens will be given the Mol2 type N.4 (appropriate for N-terminal) rather than N.am (appropriate for amide).

—Eric


	Eric Pettersen
	UCSF Computer Graphics Lab



> On Dec 6, 2019, at 7:43 AM, Palani, Kirubakaran <Kirubakaran.Palani at fccc.edu> wrote:
> 
> Hi All, 
>  
> I have a PDB file and want to convert the PDB to MOL2 format. The PDB has missing residues which is not a problem but when I write to MOL2 format it assigns the pseudobond and I really no need of it. I tried to solve it by checking the thread but I am not getting a clear solution for my problem. Last, I am doing this by using the script as I have >1000 PDBs to process the same way so the command line would be preferred.
>  
> PS: I send you the molecule in PDB format as an example case.
>  
> Thanks in advance,
> Kiruba
>  
>  
> 
> 
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