Re: [AMBER] G quadruplex simulation

From: Sruthi Sudhakar <>
Date: Sat, 29 Feb 2020 15:32:22 +0530

I have used the following input:
parm complex.prmtop
hbond donormask :14 acceptormask :18&!.H avgout hoogsteen.dat
hbond donormask :14 acceptormask :18&!.H dist 3.5 angle 135.00 avgout

Is this right to calculate the percentage hoogsteen bond occupancy?

On Sat, Feb 29, 2020 at 11:43 AM Sruthi Sudhakar <> wrote:

> Respected group members,
> If someone is working in the G quadruplex- ligand simulations, could you
> please tell me how to obtain the percentage hoogsteen bond occupancy
> between the dG residues with each quartet? Since I am a beginner I am not
> familiar about the inpuit for this.
> Thanking you in advance.
> Sruthi Sudhakar
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Received on Sat Feb 29 2020 - 01:30:02 PST
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