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.
Mark
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