Hello everyone,
I've been having problems with the rst file generation step, which has never happened to me before. My guess is that something went wrong when I deleted some parts of the original protein structure pdb file. My group wants to see if the residues that we've selected from the original protein structure can make a stable peptide. When preparing the pdb file, I kept one of the three chains, let's call it chain A, as-is in the original pdb file, and deleted residues that are not part of the peptide-sequence in chain B. So basically we now have a short peptide chain from the original chain B binding to chain A. The third chain is just the Fe atom, which is buried in the middle of chain A cluster.
I then used pdb4amber reduce and dry command to create an amber-friendly structure.
Using tleap I was able to generate a prmtop file but not the rst7 file. That step gave me this error.
> saveamberparm AbSOD-peptide AbSOD-peptide-water.prmtop AbSOD-peptide-water.r$
Checking Unit.
FATAL: Atom .R<NTRP 1>.A<H 27> does not have a type.
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 Mon Mar 07 2022 - 15:00:03 PST
