[AMBER] top and crd file error

From: kanika sharma <ksharma997.gmail.com>
Date: Fri, 2 Mar 2012 12:29:03 +0530

Hi Amber list,

I am trying to work with my protein using Leap but when I try to create the
top and crd files, I get the message

> saveamberparm var 40_240.top 40_240.crd
Checking Unit.
WARNING: There is a bond of 38.732284 angstroms between:
------- .R<ALA 81>.A<C 9> and .R<THR 82>.A<N 1>
FATAL: Atom .R<ALA 81>.A<OXT 11> does not have a type.
Failed to generate parameters
Parameter file was not saved.


I am using the ff99SB forcefield, and I used the saveamberparm command. Any
advice on getting Leap to work with my file?

Here is the file attached


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Received on Thu Mar 01 2012 - 23:00:03 PST
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