Date: Thu, 9 Jan 2025 22:16:07 -0700
From: David A Case <david.case.rutgers.edu>
To: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>, AMBER
Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] prmtop and inpcrd file generation error:
On Fri, Jan 10, 2025, Kankana Bhattacharjee via AMBER wrote:
> Sir, here I am attaching the leap.log file and also the screenshot. Dint
> receive any error as such. But warnings present. Also, the new prmtop and
> inpcrd file is having no water information. Kindly help.
The leap.log file shows that the program doesn't know about the PYR unit.
You want to use "PYR = loadMol2 <mol2-file>", not "ligand = ..."
I don't have all your files any more, but double-check that the input pdb
file actually has waters, and that (as an example) there is no "END" card
before the waters. Use a visualization program to verify that the pdb file
contains what you want it to.
...dac
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Received on Thu Jan 09 2025 - 22:00:03 PST
