[gmx-users] Docking with PyMol and using Gromacs

[Gunnar Widtfeldt Reginsson]

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?


Thanks.
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