Re: [AMBER] water mediated H-Bond

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Tue, 1 Mar 2011 10:09:20 -0800

> Convert this to pdb file, modify pdb retain only 10 water and then use it to
> generate new topology file in tleap.

Presumably there is no box.

> When I use this topology file to visualize above processed trajectry file
> structure was not proper there is some long bonds.

Maybe there's a box in mdcrd? If so, you would need to strip
it to be compatible with the the new prmtop.


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Received on Tue Mar 01 2011 - 10:30:04 PST
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