[gmx-users] Membrane tutorial regarding,
drrahulsuresh at gmail.com
Tue Apr 10 20:21:27 CEST 2018
Performing membrane simulations using charmm36 ff. The Protein/membrane
system is constructed using charmm-gui [POPC] . The system was then used in
gromacs 2016.4 for simulation . Following the simulation tutorial,
*gmx pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter
NH2 and COOH were chosen as terminals.
But bad luck its shows a fatal error.
*There were 49308 missing atoms in molecule Protein if you want to use this*
*incomplete topology anyhow, use the option -missing*
All the missing atoms were only hydrogen.
the water model was then changed to tip3p, even the error prevails.
Why the ignh flag doesn't work here?
Can I go with -missing?
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