[gmx-users] TIP5P and crystal waters

Irem Altan irem.altan at duke.edu
Mon Mar 7 17:18:14 CET 2016


I am trying to run a simulation with TIP5P and Gromacs 5.1.2. I want to do so by keeping the crystal waters in the .pdb file. When I don’t erase the crystal waters and run pdb2gmx, I get the following error:

Fatal error:
Residue 'HO5' not found in residue topology database

This error disappears when I remove crystal waters. Why does this happen? How can I keep the crystal waters?
(Note that this is an issue only with TIP5P and other water models work without a problem)


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