[gmx-users] pdb2gmx conversion

MUSYOKA THOMMAS mutemibiochemistry at gmail.com
Mon Oct 28 11:20:08 CET 2013

Dear Users,

Whenever i convert a protein.pdb file using the following command (pdb2gmx
-f protein.pdb -o protein.gro/pdb -water spc) and thereafter visualise the
output with either vmd or pymol, i get the first amino acid residue
breaking from the main chain.

Would anyone help me understand why this is happening?


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