[AMBER] [david.case.rutgers.edu: Re: Modified residue separated in leap module]

From: David Case <david.case.rutgers.edu>
Date: Mon, 23 Jan 2017 07:52:52 -0500

I sent the message below directly to your gmail address (by mistake), and you
may not have seen it. Reposting here to the whole list.


On Sun, Jan 22, 2017, asdda asa wrote:
> I just realized that when saving the pdb file, leap read DT10 as terminal
> so it added O3',

There is a "TER" card after DT10 in your input pdb file; perhaps that needs to
be removed. You would then need to manually remove the bond between DT10
and TGP 11, and add a new one between DT10 and Y2P. (You would use the "bond"
and "remove" commands in tleap to do this.)

> which established new bonds with O3P and P atoms of Y2P (screenshot
> attached), and as a result,

There is supposed to be a bond between DT10 and Y2P: see the LINK commands
in the 1k4t file: are you adding that in? Look carefully at all the LINK
cards to make sure you are establishing the correct chemistry.


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Received on Mon Jan 23 2017 - 05:00:03 PST
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