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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