Hi all,
Hope you are doing well.
Based on a CG approximation I'm trying to set up a double bilayer system in order to run Computational electrophysiology simulations (to measure ion flux in channels).

To do this, I first need to have a fully equilibrated channel embedded in a membrane (here POPC). For that (and using martinize) I create the CG representation of my protein (using a 'complete' AA structure (no VS) ). Later and; using insane script, I managed to set up the system and was able to run the CG simulation.

Now I'm trying to convert the system into an AA representation (now using also VS), and here is where the problems start to appears.
Using pdb2gmx (pdb2gmx -f outname.pdb -vsite hydrogens -ignh) I created the atomistic topology of my protein without issues, but when I ran initram (./initram.sh -f protein-POPC.gro -p topol.top -from martini -to charmm36 -o protein-POPC_aa.gro)
I first notice some weirds 'notes':
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue VAL contains duplicate names. Relying on mapping file.
The target list for residue LEU contains duplicate names. Relying on mapping file.

And then, at soon as the first EM is launch I got the error that the number of atoms in the .top and .gro files are different:
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 190772)
does not match topology (backmapped.top, 191336)
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors

The thing is, when I used a complete AA topology (no VS) initram works without problems, so definitely the problem is with the VS part.
According to the article and the forum, VS are supported in initram, so I'm definitely doing something wrong. Should I have to use a structure possessing VS at the beggining (martinize) to create the CG structure of my protein? This sounds a bit weid though.
----
My biggest problem is that the final atomistic system (without VS and considering the double bilayers) has almost 500k atoms, so I need to use VS in order to increase the timestep in the simulations.

Hope someone can help.
Best regards from Chile :),
Carlos

Hi Navarro,

Yes, VSs should not give you any problem. My guess is that within the VAL and LEU residues (I guess the ones which contain VSs?) you have atoms with the same name. Can you check that?