Re: [AMBER] Loading RNA nucleotide (ADE) tleap error

From: David A Case <>
Date: Thu, 5 Aug 2021 15:28:01 -0400

On Thu, Aug 05, 2021, Rana Rehan Khalid wrote:

>source leaprc.ff99SB

You have a rather old version of AmberTools: we have not used leaprc files
like the one above for some time. But it is probably not related to what
you are trying to do.

>ligSeq = {ADE}
>LIG = loadpdbUsingSeq ./temp.pdb ligSeq

Why do you want to use loadpdbUsingSeq ? You should experiment with just
loadPdb until you get things working.

>loadPdbUsingSeq: ADE is not a unit!

This makes sense to me (although I almost never use loadPdbUsingSeq): your
pdb file residue is named "A", not "ADE". The "UsingSeq" code is very old, and
might still use the old 3-letter nomenclature for nucleotides. (One would
have to check the code to see.)

You can use the "list" comand in tleap to see what units are loaded.

....good luck....dac

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Received on Thu Aug 05 2021 - 12:30:02 PDT
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