Thank you so much for your help! I was able to get my rst7 with your suggestions and completed my MD simulations.
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________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Monday, March 7, 2022 6:35:52 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Failed to generate rst file in partially deleted structure
Hi,
On Mon, Mar 7, 2022 at 5:45 PM Yen Nguyen <ynguyen3.gmu.edu> wrote:
> FATAL: Atom .R<NTRP 1>.A<H 27> does not have a type.
Try removing all hydrogens from your input PDB and let LEaP build them
back in according to templates. Hydrogen name mismatch is very common
and very often confuses LEaP.
-Dan
> Failed to generate parameters
> Parameter file was not saved.
>
> Here's what was added/removed by tleap before the saveamberparm step
>
> AbSOD-peptide = loadpdb AbSOD-chainB-peptidebound-tleap.pdb
> Loading PDB file: ./AbSOD-chainB-peptidebound-tleap.pdb
> Created a new atom named: H within residue: .R<NTRP 1>
> Added missing heavy atom: .R<CLYS 15>.A<OXT 23>
> Added missing heavy atom: .R<CALA 215>.A<OXT 11>
> total atoms in file: 3340
> Leap added 8 missing atoms according to residue templates:
> 2 Heavy
> 6 H / lone pairs
> The file contained 1 atoms not in residue templates
>
> I've tried adding ions to neutralize the structure to see if it would fix the problem, but it did not. Then I've tried rerunning tleap again for 4-5 times to see if it was a software problem, but that didn't work as well. So I honestly don't know what to do next.
>
> I'd greatly appreciate any help.
>
> Thank you.
>
> Yen Nguyen
> Graduate Research Assistant
> George Mason University
> Department of Chemistry and Biochemistry
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Received on Thu Mar 10 2022 - 11:00:02 PST
