Re: [AMBER] VMD prepared errors (precise error messages)

From: Daniel Roe <>
Date: Mon, 1 Jul 2013 14:12:12 -0600


On Mon, Jul 1, 2013 at 1:55 PM, Hunter Brown <> wrote:
> FATAL: Atom .R<ILE 31>.A<CD 20> does not have a type.

A quick 'desc' of the ILE unit shows that LEaP expects 'CD1' and not 'CD':

$> desc ILE.1
RESIDUE sequence number: 1
RESIDUE PDB sequence number: 0
Type: protein
Connection atoms:
 Connect atom 0: A<N 1>
 Connect atom 1: A<C 18>
Improper torsions:
A<CD1 14>

Either replace ILE 'CD' atom names with 'CD1' or easier still, strip
the CD atoms (and any attached hydrogens) from your PDB and let LEaP
build them back in for you.

> FATAL: Atom .R<L P 41>.A<OV 1> does not have a type.

I'm not sure what residue 'L P' is supposed to be but it seems really
odd that it has a space in the name. Is this supposed to be some lipid

In the future it will help if you can post at least the exact commands
you are giving LEaP. Sometimes we can guess what you are trying to do
from selected output/error messages but in general if we know exactly
how you are trying to do something in addition to what you are trying
to do we can give more specific advice.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jul 01 2013 - 13:30:02 PDT
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