AMBER Archive (2004)

Subject: Re: AMBER: AMBER7 plastocyanin tutorial problem.

From: David A. Case (
Date: Fri Aug 06 2004 - 14:09:34 CDT

On Fri, Aug 06, 2004, tarek mahfouz wrote:
> I'm a new user of AMBER and I'm trying to run the plastocyanin tutorial and
> here is what I did:
> 1- I prepared the required input files and However, since
> later on in the input file the call is for mem.lib and hicu.lib, I
> saved as hicu.lib and as mem.lib. They were read ok.

I'm lost here: the file refers to "" and "", not to any
lib files (as far as I can see)? Can you post exactly what is in your file, (and where you got it)? Here is what I see on the web site:

addAtomTypes {
  {"SM" "S" "sp3"}
loadamberparams frcmod.pcy
plc = loadPdb 1plc.protein.pdb
bond plc.87.ND1 plc.37.CU
bond plc.84.SG plc.37.CU
bond plc.92.SD plc.37.CU
saveAmberParm plc prmtop.nowat prmcrd.nowat

In particular, you should see if you have the "addAtomTypes" command in your

> and I'm concerned about the statement "residue lacking connect0/connect1"
> does it mean it will not save the N and C termini as charged?

Don't worry about this message, it really doesn't mean anything important.

...good luck...dac
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