Re: [AMBER] Leap: Nuleotides addition

From: David A Case <>
Date: Sat, 8 Sep 2018 08:31:39 -0600

On Sat, Sep 08, 2018, Aravind Ravichandran wrote:

> I am planning to simulate diffusion of nucleotides across RNA polymerase.
> For this, I have to create systems with various concentrations of NTP.
> How do I add NTP to the protein system in leap.
> Is there a way to do this in leap?
> Or should I prepare the PDB file with protein+nucleotide and then use leap
> just to prepare the system (I have the parameters for ATP and GTP)?

The second way: prepare your pdb file with protein (followed by a TER card),
then NTP. Then just run leap. (Leap has a "combine" command, but its use is
pretty specialized. Generally, users do manual editing of the input pdb file
to make systems out of component parts.)

...hope this helps...dac

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Received on Sat Sep 08 2018 - 08:00:02 PDT
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