On Thu, Oct 8, 2015 at 11:48 AM, Nicholus Bhattacharjee <
nicholusbhattacharjee.gmail.com> wrote:
> Dear all,
>
> I am trying to solvate a helical structure in a custom way. With solvatebox
> or solvateoct of tleap we can only put a value of the buffer of solvent
> from the solute surface. For example with solventbox command I get a box
> size of 32.302 X 44.333 X 34.369 with a buffer of 10. However, I want a
> solventbox which has buffer of 10 in all direction except towards the
> C-terminus of the helix where I want a buffer of 50. So considering helix
> axis to be in the Y direction the box size will be somthing like 32.302 X
> 84.333 X 34.369. Can it be done with the tleap? Thank you for the help.
>
Not via "solvateBox" or "solvateOct". You will need to use a more
specialized tool (like packmol) in order to accomplish this. Then you can
feed the generated PDB file to tleap and set the box dimensions via
"setBox".
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 08 2015 - 09:00:05 PDT
