[gmx-users] charmm gui pdb to gro.

[Yogesh Sharma]

Greetings,
hey, I want to convert the charmm gui generated pdb (membrane + protein) to
gromacs readable file.  charmm generated lipids contain hydrogen atoms and
naming differences. I tried doing it manually but couldnt succeed. Is there
any script available for atom renaming and reordering?

I also tried manual packing of POPC molecules from this site (
http://wcm.ucalgary.ca/tieleman/downloads) around oriented protein
extracted from charmm gui bilayer builder but simulation was not successful
probably i couldnot pack it properly (didn't get any error though. packing
was performed using inflategro with shrinking to a final area of 74A^2).
Charmm gui generated output is working fine with water but I want to
perform complete simulation in 54A7 ff due to ligand parameters
availability. hence, i have to convert charmm gui generated output to gro
format. Is there any way around?