[gmx-users] Pdb2gmx melts molecules due to bad distances

GIANMARCO BARTALINI gianmarco.bartali at student.unisi.it
Mon Nov 27 12:04:13 CET 2017

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?
Thank you in advance,


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