[gmx-users] Editconf owerwrites name of ligand

Jan Riehm jriehm at bioinformatik.uni-saarland.de
Thu Sep 8 15:34:39 CEST 2016


I want to simulate the behaviour of a ligand in a cyp p450 enzyme with a 
present heme group. I followed the steps on 

and built and modified the appropriate files. Now after using the 
command "gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 
1.0" i checked my newbox.gro file. Here I saw that my ligand called 
"LUP" was overwritten with "HCP" (which is the name of the heme 1LUP -> 
1HCP). Even after correcting newbox.gro by hand, in the next step after 
hitting "gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o 
solv.gro" the same overwriting happened in solv.gro.

Maybe someone got a hint or a solution to that?

Thank you and best regards,


More information about the gromacs.org_gmx-users mailing list