# Topology errors: combining protein and DPC micelles

**URL:** <https://gromacs.bioexcel.eu/t/topology-errors-combining-protein-and-dpc-micelles/454>\
**Category:** User discussions\
**Created:** [July 9, 2020, 3:45pm UTC](https://gromacs.bioexcel.eu/t/topology-errors-combining-protein-and-dpc-micelles/454 "2020-07-09T15:45:37Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![katiejoyce12](https://avatars.discourse-cdn.com/v4/letter/k/7993a0/32.png) [@katiejoyce12](https://gromacs.bioexcel.eu/u/katiejoyce12)\
**Post date:** [July 9, 2020, 3:45pm UTC](https://gromacs.bioexcel.eu/t/topology-errors-combining-protein-and-dpc-micelles/454/1 "2020-07-09T15:45:38Z")

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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](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?

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [July 9, 2020, 4:02pm UTC](https://gromacs.bioexcel.eu/t/topology-errors-combining-protein-and-dpc-micelles/454/2 "2020-07-09T16:02:33Z")

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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.