[AMBER] "Atom does not have a type" despite adding .frcmod parameters

From: Erika Davidoff <erikadavidoff.gmail.com>
Date: Thu, 27 Aug 2020 15:56:25 -0400

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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Received on Thu Aug 27 2020 - 13:30:02 PDT
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