Re: [AMBER] Tleap Fatal error

From: David A Case <>
Date: Fri, 12 Mar 2021 07:54:30 -0500

On Fri, Mar 12, 2021, richa anand wrote:
>FATAL: Atom .R<U5 805>.A<OP3 29> does not have a type.
>FATAL: Atom .R<U5 805>.A<P 30> does not have a type.
>FATAL: Atom .R<U5 805>.A<OP1 31> does not have a type.
>FATAL: Atom .R<U5 805>.A<OP2 32> does not have a type.
>FATAL: Atom .R<A5 825>.A<P 32> does not have a type.
>FATAL: Atom .R<A5 825>.A<OP1 33> does not have a type.
>FATAL: Atom .R<A5 825>.A<OP2 34> does not have a type.

Your RNA molecules have terminal monophosphates, which is not the default.

If you are using leaprc.RNA.OL3, just add the following line to your tleap
script, *after* the "source leaprc.RNA.OL3" command:

    loadOff terminal_monophosphate.lib

If you are using leaprc.RNA.LJbb, you should edit your input PDB file, to
name residues 805 and 825 UMP and AMP, respectively.

(Dan, Christina: the terminal_monophosphate.lib file allows users to avoid
modifying files that come from the RCSB, where "U" is used for a terminal
base irrespective of whether it has an attached phosphate or not. On the
other hand, it fails if some terminal bases have phosphates and others do
not. Do you have thoughts on which is better?

I'm thinking we should teach pdb4amber to look for this, and automatically
change U -> UMP, etc. Then have the -bres option in ambpdb do the reverse.)


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Received on Fri Mar 12 2021 - 05:00:03 PST
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