Re: [AMBER] NCSU_SMD for protein-ligand complex pulling

From: M RCC <>
Date: Sat, 1 Sep 2018 15:55:20 +0530

Thanks, Feng.
In this case, what would be path array?
distance or coordinate?

On Sat, Aug 25, 2018 at 8:45 PM M RCC <> wrote:

> Dear Amber users,
> Am trying to do SMD using the ncsu_smd code, trying to follow the LCOD
> tutorial.
> I have a trajectory of 200ns simulation Protein-ligand complex. planning
> to pull ligand from different frames of trajectory and calculate the
> average work done to remove the ligand.
> I have few basic questions starting from placing the protein-ligand
> complex and perform the calculation.
> Generally in Gromacs protein will be placed on one corner of the
> rectangular box and pull the ligand in the lengthiest direction with
> explicit water. How can I do the same in amber?
> How can I define the group of atoms? two sets as ligand to pull and
> protein atoms to restraint? path?
> and how to define the direction pulling in ncsu method.
> I red the tutorial and still am not clear.
> If I am wrong, Kindly suggest me which of the methods I can follow.
> Thanks in advance
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Received on Sat Sep 01 2018 - 03:30:02 PDT
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