Carry out a simulation of insulin of a silica surface

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1

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GROMACS modification: Yes/No
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Hi,

I would like to carry out a simulation of insulin on a silica surface. I have devised the following procedure to carry out the necessary simulation but would like to know if I am missing out anything.

  • Firstly, use the CHARMM gui pdb reader so that I can select the correct insulin monomer (as it allows you to select just chains A and B from a dimer or hexamer model) and have it in the correct protonation state.

  • Secondly, use the CHARMM gui nanomaterial builder to make a silica that is of the right size and protonation state. VMD to position protein correctly, save as pdb.

  • Thirdly, use the Multi Component Assembler to combine the two files generated from steps 1 and 2.

From hereon follow the membrane tutorial but without all the shrinking and expanding (because that is only relevant for lipids and for inserting a protein into a membrane) using the files generated from Step 3.

Is this the correct procedure to carry out a viable simulation?

I have found issues in having a single file with the orientated protein on the silica surface on VMD. I attempted to a obtain a single file for this using the Multicomponent Assembler and obtained CHARMM input files but need gromacs input files to run the simulation on Ubuntu.Do I require the Multi - Component Assembler or can I carry out a simulation with the files obtained from Step 1 and 2? Does anybody know how to merge PDB files together. e.g. insulin and silica in my case. Or is there a method of carrying out the simulation without merging the files?

I am relatively new to this and any advice would be much appreciated and go a long way to helping me understand.

2

The membrane tutorial has no relevance here and certainly the .mdp files are inappropriate as CHARMM uses different settings from GROMOS.

Position both species in a box of the same dimensions with editconf and then simply concatenate the files.

3

Hi,

Thank you for your reply. If the files generated from CHARMM uses different settings than Gromacs how would I proceed with the simulation on Ubuntu as my mdp files would be generated from CHARMM gui?

I would really appreciate your response and thank you for answering my previous question.

4

Inputs produced by CHARMM-GUI should be used, unmodified. They are correct.

My statement above was specifically in response to your mention of my tutorial - there is nothing in that tutorial that is of use to you.

5

Thank you for your response. I am assuming that ‘unmodified’ would refer to using the files as would be received from the CHARMM-GUI website?

Lastly, am I correcting in my thinking that I would generate my silica surface from the Nanomaterial builder and obtain my desired insulin monomer from the CHARMM-GUI PDB reader. Following this, use both the files generated and assemble them using the Multi Component Assemble or can I just merge the PDB’s files in a single PDB file using VMD and then carry out my simulation?

Also, if the membrane tutorial is of no use, I would like to carry out energy minimisation and equilibration steps but do my commands completely change as it is not an mdp file?

I really appreciate your response, I am relatively new to CHARMM GUI and have worked through GROMACS tutorials but carrying out my own simulation is proving a difficult task as I am relatively new to this.

6

Correct. I say this because I have received more emails than I can count from people who take some CHARMM-GUI output and then try to hack it to pieces to follow one of my tutorials, when CHARMM-GUI has done all the preparatory work they need. Their files should be used directly.

As for assembling your system, I have never used those modules in CHARMM-GUI. If you have problems with them or need advice, that’s a question for their core developers.

Nothing is ever different about the mechanics here. grompp to produce a .tpr from the coordinates, topology, and .mdp files, then mdrun to run whatever the process is.

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7

Thank you for your time, I will proceed with my simulation and hopefully it is successful. If I do incur any errors then I hope you do not mind me asking for advice as so far this has been really helpful with my understanding.