[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs

Payman Pirzadeh ppirzade at ucalgary.ca
Sat Dec 1 21:14:18 CET 2012


I am trying to generate a topology file for my protein which has three
disulfide bonds using ffG53a5. I realized in the topology file that the
force field parameters for bonds, angle and dihedrals of my S-S bonds are
missing. I found the following thread about this issue:


Using version 4.5.4, I typed 

grompp -p topol.top -pp topol-processed.top -f systemem.mdp -c

to generate the processed topology file. These terms are still missing in
the processed topology file, but grompp complained nothing. Am I safe? Is
there still sth going on that takes care of the missing terms in the
topology file?

Thanks for your help.





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