[gmx-users] Membrane tutorial regarding,

Justin Lemkul jalemkul at vt.edu
Tue Apr 10 20:24:06 CEST 2018

On 4/10/18 2:21 PM, RAHUL SURESH wrote:
> 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*

You shouldn't be doing this. CHARMM should not be used with SPC, and in 
fact if you built the system with CHARMM-GUI you have all the topologies 
and input files necessary to proceed directly with energy minimization, 
equilibration, etc.


> 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


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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