GROMACS modification: Yes/No
Here post your question
I have created topology from pdb2gmx command and all the required residue/bond/angle are defined in rtp entries of charmm force field. Now I want to use this topology in martini force field but bond and angle section created wont be having bond length/angle and their potential values that I have defined in bonded section of charmm force field for atom of my system. So although this topology will work fine with charmm force field but as there is no bonded entries section in martini so I need to give all these details in itp file itself.
Is there is any way to include these details in topology file using pdb2gmx or any other command.
Parameters not explicitly written to the topology are referenced from
ffnonbonded.itp. Why are you trying to combine CHARMM bonded parameters with the MARTINI force field? They’re not compatible.
Thanks for replay
Actually I want to create topology that will work for martini force field. My molecule is very large so I have used charmm just to create topology using pdb2gmx. I have define my residue specific atomtype and connection in .rtp folder. I have given bond and angle parameter in ffnonbonded.itp explicitly. So as a output I am getting all connection in topology, if it was possible to write parameter also along with connection,that topology could have been used for martini force field.
Thanks and regards
There are MARTINI tutorials you should be following. What you’re doing doesn’t make any sense to me.