Re: [AMBER] {SPAM?} trajectory of mutation generation (Geng Dong)

From: Matthew Guberman-Pfeffer <>
Date: Sun, 17 Oct 2021 08:51:58 -0400

Hi Geng,

A quick idea, though there are probably more rigorous ways of doing this: Use the change command in ParmEd to zero out the non-bonded terms for the sidechain atoms except the beta carbon. Then, use the change command in ParmEd to give the beta carbon effective charge and LJ parameters to mimic the methyl of alanine. Finally, write a new topology file. This altered topology can be used with your original trajectory to assess the energy (e.g., with esander).


> On Oct 17, 2021, at 5:32 AM, 东庚 <> wrote:
> *Message sent from a system outside of UConn.*
> Hi all,
> I would to calculate the difference of nonbond interaction between wildtype and mutation (to alanine) protein. I have a trajectory for wildtype. Can I generate a mutated (to alanine) trajectory, directly. I know that the mutated trajectory can be generated by in alanine scanning calculation. What program is used in
> Best,
> Geng
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Received on Sun Oct 17 2021 - 06:00:02 PDT
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