Re: tutorial on plastocyanin

From: David A. Case <>
Date: Wed 2 Oct 2002 07:48:27 -0700

On Tue, Oct 01, 2002, Ioana Cozmuta wrote:

> Although I know that in amber7 the default
> loaded force field is parm99...

minor point: there is no default force field for LEaP in amber7 -- you always
have to specify one by sourcing a "leaprc" file.

> >> loadAmberPrep
> Loading Prep file: ./
> Unexpected EOF: discarding residue (STOP )

The message about UNKNOWN ATOM TYPE is innocuous. The real error is the
"Unexpected EOF:..". It looks like you have an extra "STOP" line in the
file (?) Without seeing the file, I cannot say more.
> (BTW, I assume that the
> files mem.lib and hicu.lib in the file from the tutorial web page
> are actually and generated previously).

No. In "amberese", files ending in ".lib" are off files; in this context,
files ending in ".in" are "prep input files".

> With this modification leap is running but there are some messages
> that it spits out besides the UNKNOWN ATOM TYPE:CU that I would like to
> understand if they are normal or not:

This is probably innocuous.

> when loading the PDB file there is a long list of messages like the one
> below:
> (Residue 1:ASP, Nonterminal, was not found in name map.)

This is standard.

> then when generating the topology/Building improper torsion parameters
> there is a long list of Warnings
> **Warning: No sp2 improper torsion term for H-H-N3-H atoms are H1 H2 N H3
> and then right in the end Residues lacking connect0/connect1 -these don't
> have chain types marked
> res total affected
> CASN 1
> NILE 1
> (the last two are the C and N of the terminal residues so I assume it is
> normal to have this message out).

That is correct.

The CU atom is (or should be) defined in the frcmod.pcy file. Don't worry:
if LEaP doesn't know how to make bonds to CU (etc.) it will complain and
not write out a prmtop file.

I think the UNKNOWN ATOM stuff can be fixed by defining these atoms in
an "AddAtomTypes" command to LEaP, before reading the frcmod file. When
that is missing, the program won't know the atomic number and hybridization
of CU, but that is not needed anyway. I'll look into revising or eliminating
the warnings.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Wed Oct 02 2002 - 07:48:27 PDT
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