Hello,
I strongly recommend you to update to the newest Amber18 to use the new NFE
module to
run the SMD, it is more systematic in the format and also fix several bugs.
Basically you just need to define everything inside the &smd block, check
the manual for details, it also has example input files.
I am not sure if you need to put the protein at the corner of the box,
since the distance is
calculated based on PBC, I think where you put the protein doesn't make
real difference.
For defining group of atoms, just use COM_DISTANCE of DF_COM_DISTANCE as
reaction
cooridnate, the direction of pulling just follows your definition in the
path array.
Best
Feng
On Sat, Aug 25, 2018 at 11:19 AM 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
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>
--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Sat Aug 25 2018 - 09:30:02 PDT
