Dear Amber users,
I am new to computational modeling and have an issue I've been trying to
solve. I am working with a PDB of a protein that has mostly standard
residues and one non-standard HETATM called PCA that contains 8 atoms. To
get the parameters for this non-standard residue, I made a separate PDB
with the one residue, added hydrogens to it and used antechamber to
generate a mol2 file:
antechamber -i ccl2_fragH.pdb -fi pdb -o ccl2_fragH.mol2 -fo mol2 -at amber
-c bcc
Then I used parmchk2 to generate a modified force field parameters file
that has a lot of parameters:
parmchk2 -i ccl2_fragH.mol2 -f mol2 -o ccl2.frcmod
Then I have a tleap script that includes the lines
loadamberparams ccl2.frcmod
ccl2 = loadPdb ccl2.pdb
and proceeds to add a peptide to the system and solvate it. When I run
this, I get errors for all eight atoms in the non-standard residue:
Unknown residue: PCA number: 0 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: PCA sequence: 1
Created a new atom named: N within residue: .R<PCA 1>
Created a new atom named: CA within residue: .R<PCA 1>
Created a new atom named: CB within residue: .R<PCA 1>
Created a new atom named: CG within residue: .R<PCA 1>
Created a new atom named: CD within residue: .R<PCA 1>
Created a new atom named: OE within residue: .R<PCA 1>
Created a new atom named: C within residue: .R<PCA 1>
Created a new atom named: O within residue: .R<PCA 1>
...
FATAL: Atom .R<PCA 9>.A<O 8> does not have a type.
FATAL: Atom .R<PCA 9>.A<C 7> does not have a type.
FATAL: Atom .R<PCA 9>.A<OE 6> does not have a type.
FATAL: Atom .R<PCA 9>.A<CD 5> does not have a type.
FATAL: Atom .R<PCA 9>.A<CG 4> does not have a type.
FATAL: Atom .R<PCA 9>.A<CB 3> does not have a type.
FATAL: Atom .R<PCA 9>.A<CA 2> does not have a type.
FATAL: Atom .R<PCA 9>.A<N 1> does not have a type.
I have attached: ccl2.pdb, the original protein file (straight from the
database); ccl2_fragH.pdb, the file with the one residue; ccl2.frcmod; and
my tleap script.
Thank you for your help!
Best,
Erika
*Erika J. Davidoff *
*Rutgers University*
Department of Biomedical Engineering
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- application/octet-stream attachment: ccl2.pdb
Received on Thu Aug 27 2020 - 13:30:02 PDT
