[gmx-users] Membrane tutorial regarding,

RAHUL SURESH drrahulsuresh at gmail.com
Tue Apr 10 20:21:27 CEST 2018

Dear Users,

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
-water spc*

NH2 and COOH were chosen as terminals.

But bad luck its shows a fatal error.

*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?

Thank you

*Rahul Suresh*
*Research Scholar*
*Bharathiar University*

More information about the gromacs.org_gmx-users mailing list