Re: [AMBER] Capping RNA

From: David A Case <>
Date: Thu, 11 Apr 2019 10:03:46 -0400

On Thu, Apr 11, 2019, Mihaljevic-Juric Paula (Mme) wrote:

>I would like to use AMBER for RNA simulations. I am trying to convert
>CHARMM files to AMBER, so I am not sure which terminal patches to use in
>For example, if there are missing 5' and 3' terminal ends of the RNA, how
>should I cap it? In CHARMM I used 5PHO and 3PHO patches, as if I would
>have phospate groups with OH.

Amber doesn't use "patches" to cap end groups in the way that CHARMM
does. We have 5' and 3' terminal residues that are already terminated.
These are chosen by default whenever a terminal residue is located.

If you have a 5' nucleotide with a mono-phosphate, then a different
procedure is needed. See section 3.2.3 in the Reference Manual for

...good luck...dac

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Received on Thu Apr 11 2019 - 07:30:02 PDT
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