Re: [AMBER] Problem with AMP atom separating in equilibration

From: David A Case <>
Date: Tue, 8 Jan 2019 09:01:02 -0500

On Mon, Jan 07, 2019, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
>I am trying to run an RNA stem-loop with AMP as a ligand (from PDB: 1RAW).

> However, in an unrestrained heating phase of equilibration the run fails
>(Amber 18) and the final state PDB file shows the above HOP3 separated
>from its O3P by 3.48A (starts at 0.99A atom center to atom center).

>How should approach debugging this?

First, fire up parmed, and see if there is indeed a bond between these
two atoms. You can also manually look at the mol2 file you made for the
AMP residue to see if the required bond is there.

Are you using SHAKE during your MD runs? You might see if that makes a
difference. If SHAKE is off, it's possible (although unlikely) that a bad
initial geometry could lead to what you observe.

...good luck...dac

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Received on Tue Jan 08 2019 - 06:30:01 PST
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