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 aren’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
