Good morning everyone.
I am having the same problem. I posted my question but it is waiting
approval to be posted as i wrote it too long, pethaps.
Thank you
Regards
On Fri, 28 Aug 2020, 3:56 am Erika Davidoff, <erikadavidoff.gmail.com>
wrote:
> 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 - 16:00:02 PDT
