[gmx-users] Pdb2gmx melts molecules due to bad distances
jalemkul at vt.edu
Mon Nov 27 14:36:54 CET 2017
On 11/27/17 6:04 AM, GIANMARCO BARTALINI wrote:
> Hello guys, I produced a system "protein + lipid membrane" using the online
> tool CHARMM-GUI. Since I need to use the Amber force field, I added the
> Lipids17 force field inside Gromacs. The implementation should work fine,
> since the conversion of an equilibrated structure produces a nice and
> correct gro file. But when I try to convert the (not minimized) PDB file
> that I get from CHARMM-GUI using pdb2gmx, I get a gro structure where many
> lipid molecules are melted together (due to their bad distances). If I use
> this structure for a minimization, the calculation stops due to bad
> energies. Do you know how to solve this issue?
This isn't a pdb2gmx problem so much as it is a quirk of how CHARMM-GUI
creates lipid membranes. There is almost always overlap between tail
atoms in the different lipid leaflets. The CHARMM minimizer deals with
these just fine, but GROMACS almost always chokes. The reason is that
GROMACS sets a rather aggressive default EM step size of 0.02 nm,
whereas the CHARMM minimizer defaults to 0.002. Lower the value of
emstep and see if it proceeds correctly. That has always worked for us.
Justin A. Lemkul, Ph.D.
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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