[gmx-users] Docking with PyMol and using Gromacs

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 12 00:23:11 CET 2009

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.


> Thanks.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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