Re: [AMBER] Error in xleap: water molecules

From: David A Case <>
Date: Sat, 9 Jan 2021 16:10:50 -0500

On Sat, Jan 09, 2021, Eduardo R. Almeida wrote:
>I used the symbol "..." to show that the file continues above and below the
>snippet that I presented in this message.

But can you show the *first* error or two?

I'm thinking you will have to put the PDB into a Dropbox or equivalent.
I've used tleap on an input pdb file that had 92,000 water molecules and
about 1 million atoms. But packmol might be doing things that are odd with
really big files (systems that are nominally too big for the PDB format).

But what I would do is just what you could do as well: start by removing
waters from the end of the file (if they are at the end) to see if you can
get rid of the error. The put back just enough to trigger the error. This
will localize the problem. (This is why I think it may help to report the
first error you see.)


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Received on Sat Jan 09 2021 - 13:30:02 PST
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