Re: [AMBER] Fw: covalent molecule and modified residue parameters

From: Sarah Jane <>
Date: Mon, 7 Sep 2020 15:09:36 +0000 (UTC)

 Hi Dac,
Thank you, it worked.And now how to connect them.
> HAR = sequence {ACE HAR NME}
Warning: One sided connection. Residue (HAR) missing connect0 atom.
Warning: One sided connection. Residue (ACE) missing connect1 atom.> desc HARUNIT name: ACEHead atom: nullTail atom: nullContents:R<ACE 1>R<HAR 2>R<NME 3>> set HAR name "HAR"> set HAR.1 name "HAR"> set HAR.1.N1 name "N"
Error: HAR.1.N1: not a container (e.g. residue)usage:  set <container> <parameter> <object>   or:  set default <parameter> <value>
Thanks,Sarah On Monday, 7 September 2020, 13:48:02 BST, David A Case <> wrote:
 On Mon, Sep 07, 2020, Sarah Jane wrote:
>  I edited mol2 file and uploaded like mentioned in 'help loadMol2'.
>  I tried 'desc' command and attached leap.log file.
>  Please advice.

Here's your problem:

> HAR = loadMol2 HAR.mol2
> HAR = loadAmberParams HAR.frcmod

The first line is loading the mol2 file into the unit called "HAR", but the
second line is overwriting that with the force parameters.  You generally
don't need to name the PARMSETs (frcmod files) that you read in, but you
certainly can't re-use the "HAR" name that you already used for the mol2 file.

Simplest: just remove the "HAR =" part from the second line above.


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Received on Mon Sep 07 2020 - 08:30:02 PDT
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