On Sat, Jan 13, 2024, Siavoush Dastmalchi via AMBER wrote:
>
>I am trying to run an MD on a protein solvated in guanidinium Cl
>solution. Would you please let me know where I can find a file like
>8Murea.off for guanidinium Cl with a concentration of ~ 3 M and use it to
>solvate my protein in the simulation box. Or you may suggest how I can make
>it. I found gromacs gnd.itp, gnd3M.gro and gnd5M.gro files but I couldn't
>convert them to amber top and structure files. Looks like parmed hasn't
>been properly configured on my system.
Can you say exactly what you tried with parmed, and what the result was?
...thanks...dac
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Received on Wed Jan 17 2024 - 09:00:02 PST
