Re: problem with tleap

From: David A. Case <>
Date: Tue, 8 Apr 2003 09:12:34 -0700

On Tue, Apr 08, 2003, S.Swaminathan wrote:

> FATAL: Atom .R<PRO 2>.A<HB1 15> does not have a type.

proline should not have an HB1 atom; take a look at the residue libraries.
Since you are just starting out, I recommend letting LEaP add the protons
for will get the names right.

> how do i create libraries for new residues for eg. HEM?

See the $AMBERHOME/dat/contrib directory, or Richard Bryce's web page (link
is on the amber web page.)

> B.the number indicated in case of :
> FATAL: Atom .R<HEM 10479>.A<FE 1> does not have a type
> is 10479, but in reality, there is no such residue number in the
> atom file.

LEaP adds 10000 to residues in subsequent chains, in order to obtain unique
residue numbers.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Tue Apr 08 2003 - 17:53:01 PDT
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