Thanks, Feng.
In this case, what would be path array?
distance or coordinate?
On Sat, Aug 25, 2018 at 8:45 PM M RCC <mkr3j2c1.gmail.com> 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
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Sep 01 2018 - 03:30:02 PDT
