[gmx-users] pdb2gmx , or equivalent

[Ling Chan]

Hello Colleagues,

I would like to run Gromacs on some proteins that I have prepared. I see that you can obtain Gromacs input files using pdb2gmx. Just wonder if one can prevent pdb2gmx from tempering with your protein? I mean, pdb2gmx does a bunch of clean ups. I would like it to skip the clean up stage.

I see that one can either let the clean up happen automatically, or have you tell it interactively whenever there is a decision to make. I would just like it to respect my structure – in the sense that no hydrogen is added or removed.

Thank you.

Ling Chan

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