GROMACS modification: Yes/No
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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.
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.
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.
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.
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.
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.
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.