[gmx-users] Converting pdb from CHARMM-GUI with pdb2gmx

Lewis Martin lewis.martin44 at gmail.com
Thu Mar 22 04:40:27 CET 2018

To answer my own question, the MacKerell website has the correct parameter
files for GROMACS to use via pdb2gmx:
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs , put this in the
same directory.

I'm now following instructions from various gromacs mailing list posts and
tutorials. Specifically, to remove water and ions (since .itp files already
exist for these) and then run pdb2gmx. Following this, add lines like this:
#include "charmm36-jul2017.ff/tip3p.itp" for water and ions to your new
topol.top, and lines like this:
SOL             21930
NA                 57
CL                 63
to the [ molecules ] section.

Finally, grompp gives this error:

gmx grompp -f mdout.mdp -c myfile.pdb -p topol.top
number of coordinates in coordinate file (myfile.pdb, 114864) does not
match topology (topol.top, 118925)

How is grompp counting the number of coordinates in the topology file? It's
suspiciously close to being right... But it doesn't add up to the number of
ions, lipid, water, or protein atoms. Is it just number of molecules x
number of atoms in .itp file? Should each POPC residue have a TER record
after it since they're not linked in a chain?

On Wed, Mar 21, 2018 at 3:04 PM, Lewis J Martin <lewis.martin44 at gmail.com>

> Hi all,
> I'd like to run simulations using virtual site hydrogens to allow
> increased timestep. I can't find a tool for generating HMR hydrogens
> (common in Amber) so Im looking at vsites.
> For convenience I'm using CHARMM-GUI. Is pdb2gmx the correct tool to
> introduce vsites? Using it, I keep coming across:
> 'Atom OT1 in residue VAL 364 was not found in rtp entry VAL with 16 atoms
> while sorting atoms.'
> This suggests a problem with the terminal patch, yet using the -ter flag
> and choosing the terminal patch  results in the same issue. Inspection of
> the file 'aminoacids.c.tdb' suggests that OT1 is indeed included in the
> parameters.
> So I turned to other tools like psf2top and ParmEd. psf2top works
> beautifully, but can't include vsites. Can you add vsites directly to
> .top/gro files without pdb2gmx?
> Any info is appreciated.
> Cheers
> Lewis

More information about the gromacs.org_gmx-users mailing list