Re: [AMBER] Modified AA residue without NH2 end.

From: Carlos Simmerling <>
Date: Thu, 12 Mar 2020 06:51:55 -0400

Is this for a low pH simulation? It's not clear exactly what the end atoms
Did you also load the prmtop file to see the bonds? Some programs use
distance to select bonds, which can be inaccurate with an initial
structure. Try loading both the prmtop and coordinates into a program like
Vmd. You can also use parmed to show the bonds that are present.

On Thu, Mar 12, 2020, 6:41 AM Petro <> wrote:

> Hi list.
> I am trying to make a modified AA which has no NH2 end.
> COOH end atom names are:
> C1, O3, H12, O,
> mc file is :
> -----------------------
> CHARGE -1.0
> --------------------------
> The residue is made using GAFF FF. I have added missing parameters to
> connect GAFF residue to AMBER protein and tleap running without errors.
> But when I load rst file into pytraj/nglview. there is not bond between N
> atom of protein and C1 atom of my residue.
> What am I missing there?
> Thank you.
> Petro.
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Received on Thu Mar 12 2020 - 04:00:03 PDT
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