Re: [AMBER] Errors regarding generation of parameter file

From: David A Case <>
Date: Mon, 19 Nov 2018 08:20:23 -0500

On Mon, Nov 19, 2018, shivangi agarwal wrote:
>While generating ligand parameters, I am facing some angle parameters
>errors, I used the following commands
>* parmchk -i 2888695.mol2 -f mol2 -o 2888695.frcmod*

Examine this frcmod file with a text editor to see what its contents are.

Also, you should upgrade to the current version of AmberTools18: the
"parmchk" command has been removed some time ago (in favor of parmchk2).

>*> LIG = loadmol2 2888695.mol2*
>Loading Mol2 file: ./2888695.mol2
>Reading MOLECULE named LIG

>*> loadamberparams 2888695.frcmod*

>Could not find angle parameter: c1 - s - c2
>Could not find angle parameter: c2 - c1 - ha
>Could not find angle parameter: c2 - c1 - ha
>Could not find angle parameter: n1 - c1 - s
>Building proper torsion parameters.
> ** No torsion terms for c1-s-c2-c2
> ** No torsion terms for c1-s-c2-c1
> ** No torsion terms for c1-c1-s-c2
> ** No torsion terms for c2-c1-n1-c1
> ** No torsion terms for c1-n1-c1-c1
> ** No torsion terms for c1-c1-n1-c1
> ** No torsion terms for s-c1-n1-c1
> ** No torsion terms for n1-c1-s-c2

First thing to do is to see if these parameters are in the frcmod file.


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Received on Mon Nov 19 2018 - 05:30:03 PST
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