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

From: Bala subramanian <bala.biophysics.gmail.com>
Date: Mon, 26 Mar 2012 17:23:49 +0200

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.top 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.

C. Balasubramanian

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Received on Mon Mar 26 2012 - 08:30:04 PDT
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