Hi,
I want to perform molecular dynamics simulation of protein-RNA complex at deifferent pH condition in gromacs.
When I am using Amber force field, It is not detecting protonated residues while OPLSaa force field is not detecting nucleotides.
Is there any other software available to perform this simulation??
Dear sir,you can use charmm force field and dock the complex in HADDOCK along with conversion of nucleotide symbol to Gromacs defined molecules which is mentioned in log files of gromacs using pdbeditor.i had performed for DNA-Protein complex last year.even you can use OPLS or AMBER force field also.
My system is protonated. IF I am using force field other than OPLS, that protonation state is changing.
Hi,
I'm pretty sure you could do what you want using AMBER software.
If you could provide more information about what you want to do, maybe I can help. Or you can contact with AMBER developers using their mailing list
http://lists.ambermd.org/mailman/listinfo/amber
Have a nice day.
Karolina
Hi, Karolina.
I want to perform the simulation of protein-RNA complexes at different-2 pH conditions.
I used OPLSaa force field to do that for protein alone, but when I am doing that for protein-RNA complexes, it is showing errors.
Amber94 is asking me to delete all extra hydrogen atoms, which I have added during protonation of protein wherever OPLSaa is not detecting nucleotides.
So, How can I do that without modifying force field?
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