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

From: David A Case <>
Date: Mon, 28 Sep 2020 08:23:12 -0400

On Mon, Sep 28, 2020, Sarah Jane wrote:

>Error: Could not find bond parameter for: N2 - OH
>Error: Could not find angle parameter: H - N2 - OH
>Error: Could not find angle parameter: N2 - OH - HO
>Error: Could not find angle parameter: CA - N2 - OH
>Error:  ** No torsion terms for  H-N2-OH-HO
>Error:  ** No torsion terms for  CA-N2-OH-HO

You will need to assign parameters for the above, which look like they
involve the connections between your HAR residue, and the surrounding
ones. There are three strategies:

1. See if the people at the RED site can help -- they must have
encountered this problem before.

2. Run parmchk2 asking for Amber atom types.

3. Look in gaff2.dat for the corresponding atom types (which will be
lower case), and manually create a frcmod file with the above force
field terms, by changing lower case gaff2 types to upper case Amber atom

....good luck....dac

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Received on Mon Sep 28 2020 - 05:30:02 PDT
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