I am currently working on silica slab preparation. For that I have generated the supercell in materials studio, but when I tried to export this into pdb, some unusual bond connectivities developed. Now I have found a way to circumvent the problem, I saved the file as cif and then used open babel to convert it into pdb.
Is this correct? I will be using the slab for md studies in gromacs
Martin Klvana
There is no connectivity information in ATOM section of PDB file. "Unusual connectivity" is either visualization artifact (bonds drawn between atoms within certain distance) or specified in CONECT section of PDB file (irrelevant for generating topology file for MD simulation).
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