[gmx-users] Re: topology and coordinate file not matching after grompp

chinnu657 cma1g09 at soton.ac.uk
Mon Aug 5 11:38:33 CEST 2013

Hi Justin,
The simulation is running fine for this task.

There's something additional I want to do and I'd like to know how you'd
approach it. I want to add charges to each of the protein so that I can
observe how the respective protein interacts with their respective charge
cloud. The proteins im using are 2CDS.pdb and 1AKI.pdb from the RCSB bank. 

>From what I figured, I tried using genion under the impression that I could
replace the solvent molecules with CL ions but I don't think this worked. 

I'd really appreciate it if you could share your thoughts on this


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