[gmx-users] Docking with PyMol and using Gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 12 00:33:19 CET 2009

Justin A. Lemkul wrote:
> Gunnar Widtfeldt Reginsson wrote:
>> Hi.
>> I am a new user of Gromacs.
>> My question is both PyMol and Gromacs related.
>> I tried the PyMol users mailing list but couldn't find anything.
>> I have a small organic molecule that I am inserting into DNA in pymol.
>> I have the DNA as one pdb file and the organic molecule as another pdb 
>> file. I open the DNA file in pymol and then load the organic molecule. 
>> After docking the organic molecule I write "save name.pdb"
>> When viewing the name.pdb file in pymol there are some bonds between 
>> the organic molecule and the DNA that I don't want. Somehow pymol 
>> creates them and I don't see those bonds in the name.pdb file when I 
>> open it in a text reader.
>> I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file 
>> of the organic molecule with topolbuilder 1.2 , and unite those .gro 
>> files and convert into a .pdb with editconf The newly created pdb file 
>> still has those unwanted bonds.
>> My question is:
>> Can I ignore those bonds?
>> If not, how can I prevent pymol making those bonds?
> For the purposes of simulation, a bond is defined in the topology, not 
> the coordinate file.  What you are seeing is simply an artifact of the 
> heuristic methods that visualization programs use to guess where bonds 
> "should" be.

Indeed. It's a case of the visualization programs doing "what you want" 
for simple usage, which is less suited for more complex usage. Given the 
complexity of learning to use such programs, it seems few people 
remember the caveats in the documentation about the generation of 
"bonds", or stop to wonder where they come from :-)

It's also no wonder that many research groups who do MD use the 
simulation package most familiar to the leader (from their own doctoral 
days?), rather than the package best suited in the abstract to the task 
at hand, since the former strategy makes the best use of the accumulated 
wisdom of the senior researchers.


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