Re: [AMBER] DNA Strand Broken after minimization

From: David A Case <>
Date: Tue, 13 Jul 2021 16:15:37 -0600

On Tue, Jul 13, 2021, Sumon Naskar wrote:

>I'm sure no bond is present between the P-atom and the O3'. The usual
>bond length between P and the O3' atoms is around 1.6 Angstrom but in my
>structure where the DNA strand is terminated, the distance between the
>P-atom and the O3' atom is 3.9 Angstrom. Here are the snapshots from the
>PYMOL visualization software.

First task: determine if the bond is present in the prmtop file: use the
printBonds actin in parmed.

Second task: if the bond is not there (seems most likely) try to figure out
why. It seems likely that you need to use the "bond" command in tleap to
create the missing bond.


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Received on Tue Jul 13 2021 - 15:30:02 PDT
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