[AMBER] how to create periodic box similar to TIP3PBOX?

From: Junjian Miao <junjianmiao.gmail.com>
Date: Fri, 4 Mar 2011 09:32:35 +0800

Hi all,

 

I want to create a benzene periodic box to simulate macromolecules using the following actions and steps,

 

loadoff bnz.lib

init = copy BNZ

solvatebox init BNZ 30 iso

saveamberparm init bnzbox.prm bnzbox.rst

 

i checked the bnzbox.rst, surprisingly, it is not a cubic box, why?

 

then i performed NVT, NPT equilibration. because of diffusion of benzene, i processed the final .rst file with ptraj.

 

ptraj benbox.prm << EOF

trajin density.rst

center

image origin center familiar

trajout benbox.pdb pdb

EOF

 

then i entered into tleap, issued commands as follows,

 

solbox = loadpdb benbox.pdb

solvatebox mymol solbox 12

 

since my molecule is very large, so tleap utilizes 4 box to surround the molecule, but there are significant gaps between boxes. however, for the TIP3PBOX, CHCL3BOX, NMABOX, etc. there arení»t gaps, although they are relatively small boxes, why?

 

how to create TIP3PBOX-like solvent box? and further, how to load it automatically when using tleap?

 

Any suggestions are greatly appreciated.
Thanks in advance!

Regards,

 

Junjian Miao
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Received on Thu Mar 03 2011 - 18:00:03 PST
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