The pdb2gmx program is complaining...

Friday, 09 September 2005

The pdb2gmx program is complaining about long bonds and/or missing atoms. What should I do? There are probably atoms missing earlier in the .pdb file which makes pdb2gmx go crazy. Check the screen output of pdb2gmx, as it will tell you which one is missing. Then add the atoms in your pdb file, energy minimization will put them in the right place, or fix the side chain with e.g. the WhatIF program.

 

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