Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues

From: Ross Walker <>
Date: Mon, 26 Mar 2012 09:37:02 -0700

Dear Bala,

You are not following the tutorial properly. Please read it again carefully.
You need to load both the lib file and a frcmod file containing the
parameters for copper and any related bonds, angles, dihedrals etc.

See the beginning of section4.

All the best

> -----Original Message-----
> From: Bala subramanian []
> Sent: Monday, March 26, 2012 8:24 AM
> To: AMBER Mailing List
> Subject: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard
> Residues
> Hello,
> I am trying to reproduce tutorial A1. In section two, it is shown how
> to
> use leap to create a new residue (for copper). I followed the same
> procedure as given in the tutorial. creating a unit called CUA -
> editing
> the copper atom to define type and charge - saving the library as
> cua.lib.
> After creating a new residue called CUA and saving the lib file, I quit
> the
> leap and then started it again. Then i tried to create a prmtop and crd
> files for copper but leap shows me the following error.
> > loadoff cua.lib
> Loading library: ./cua.lib
> Loading: CUA
> > saveamberparm CUA cua.crd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
> WARNING: The perturbed charge: 1.000000 is not zero.
> -- ignoring the warnings.
> Building topology.
> Building atom parameters.
> For atom: .R<CUA 100>.A<CU 1> Could not find type: CU
> Parameter file was not saved.
> Herewith i have attached the leap.log file and the cua.lib (renamed as
> just
> cua) files. Kindly write me what is going wrong here.
> Thanks,
> --
> C. Balasubramanian

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Received on Mon Mar 26 2012 - 10:00:03 PDT
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