Re: AMBER: Problem in loading a PDB file in Leap - Please help me

From: tim <>
Date: Thu, 15 Apr 2004 07:53:41 +0200

> FATAL: Atom .R<DA5 1>.A<P 31> does not have a type.
> FATAL: Atom .R<DA5 1>.A<O1P 32> does not have a type.
> FATAL: Atom .R<DA5 1>.A<O2P 33> does not have a type.

the problem is the xleap DA5 unit terminates in a 'OH group while your
structure terminates with a phosphate. should be fine if you delete the
phosphate group and let xleap add the appropriate atoms

> FATAL: Atom .R< 295>.A<MG M 1> does not have a type.

your MG line in .pdb seems to be shiftet

tail -4 Ch_100.pdb
ATOM 9348 O3' THY B 147 46.246 7.648 1.090 1.00 0.00
ATOM 9349 MG MG 148 2.451 26.592 -0.651 1.00 14.63

fixing that should be enough

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Received on Thu Apr 15 2004 - 09:53:00 PDT
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