Topology errors: combining protein and DPC micelles

User discussions
1

I am simulating a protein and several DPC micelles in a box filled with water. I used the “insert-molecules” command to insert a number of micelles (m40.pdb from https://people.ucalgary.ca/~tieleman/download.html) into the box which already has the protein in it. However, I am running into countless fatal errors as I try to add ions and use the grompp command. I edited the topology file generated by pdb2gmx from my protein to include #include ‘dpc.itp’ , however the errors persisted (number of coordinates in coordinate file , or unknown atom/bond type in dpc.itp). How can I get this system to work?

Or is there a better way to integrate micelles into my box with a protein?

2

The DPC uses an OS atom type that is not part of any standard GROMOS force field. I don’t know where it comes from but it may be the deprecated GROMOS87 parameter set or a newer modification of GROMOS96. You should contact Dr. Tieleman for clarification.

As for the errors, the mismatch in coordinates and topology is almost always due to a simple bookkeeping error. Make sure you’re counting your entities correctly and updating [molecules] accordingly. The unknown bond/atom types probably come from the OS atom type I mention above.

If you’re still having problems, please post actual, complete error messages.