Your correct Carlos, the initial numbers were not properly placed. I washed the pdb successfully. Thank you!
Thanks
Debarati
________________________________
From: Carlos Simmerling <carlos.simmerling.stonybrook.edu>
Sent: Monday, September 16, 2024 10:03 AM
To: Debarati DasGupta <debarati_dasgupta.hotmail.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] reduce command
what is the source of the PDB file? perhaps the initial numbers are in the wrong column
On Mon, Sep 16, 2024 at 12:55 PM Debarati DasGupta via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
Hi all,
I am unsure when I do a reduce -Trim sys.pdb > test.pdb why are some of the H atoms being treated as carbon atoms? I have never seen this with the reduce command earlier.
Any ideas what I am doing wrong?
[cid:481da2d9-16d6-4d9e-9129-d3f364960753]
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