Re: [AMBER] Error in xleap: water molecules

From: Bill Ross <>
Date: Sat, 9 Jan 2021 13:37:22 -0800

I bet the res numbers are being chopped by reading the pdb format, and
maybe if they were shifted a position after the digits get too many
amber could handle them.


On 1/9/21 1:10 PM, David A Case wrote:
> 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.)
> ....dac
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Sat Jan 09 2021 - 14:00:02 PST
Custom Search