Re: [AMBER] [ Re: Modified residue separated in leap module]

From: asdda asa <>
Date: Tue, 24 Jan 2017 04:34:29 +0800

Dear Prof. Case,

> 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.)

Could you please to detail how to use “bond” and “remove” commands in tleap.
I am new in Amber.

>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.

The LINK commands in 1k4t file connects C3' of DT10 and O3P of Y2P and
they exist since in the original pdb file.

Thanks for help.
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Received on Mon Jan 23 2017 - 13:00:02 PST
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