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PostPosted: Fri Nov 13, 2015 9:54 am 
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Joined: Fri Nov 13, 2015 9:44 am
Posts: 5
Hi everyone,

for some PDB files, in particular the original ones from the PDB, the molecular surface in ADT is visualized correctly. However, the standard PDB files which are produced by NAMD/VMD using the CHARMM force field yield molecular surfaces in ADT which have many holes...
I attached a screenshot.

The main difference between the pdb files in format is the original pdb file some atoms are named like HE21 and in the new ones from VMD they are labelled 1HE2.

Can this be the difference? If yes, how can I change the entire namings in the file?
And is this different naming a problem for using Autodock Vina?

I look forward to hearing from you.

Best wishes,
Jadzia


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