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

[Payman Pirzadeh]

Hello,

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:

http://lists.gromacs.org/pipermail/gmx-users/2011-November/066371.html

Using version 4.5.4, I typed 

grompp -p topol.top -pp topol-processed.top -f systemem.mdp -c
protein-solvated-neutral.gro

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.

Best,

 

Paymon