Dear Sir,
After generating parameters through RED server, following errors appear:
> set default PBRadii mbondi3Using ArgH and AspGluO modified Bondi2 radii> loadoff HAR.offLoading library: ./HAR.offLoading: HAR> loadamberparams HAR.frcmodLoading parameters: ./HAR.frcmodReading force field modification type file (frcmod)Reading title:FRCMOD file generated by PyRED version JAN-2019 - q4md-forcefieldtools.org> loadoff ACA.offLoading library: ./ACA.offLoading: ACA> loadamberparams ACA.frcmodLoading parameters: ./ACA.frcmodReading force field modification type file (frcmod)Reading title:remark goes here> mol = loadpdb mol.pdbLoading PDB file: ./mol.pdbMatching PDB residue names to LEaP variables.Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA.Mapped residue ILE, term: Terminal/last, seq. number: 269 to: CILE. total atoms in file: 4096 Leap added 69 missing atoms according to residue templates: 69 H / lone pairs> saveamberparm mol mol.dry.top mol.dry.rstChecking Unit.Building topology.Building atom parameters.Building bond parameters.
Error: Could not find bond parameter for: N2 - OHBuilding angle parameters.
Error: Could not find angle parameter: H - N2 - OH
Error: Could not find angle parameter: N2 - OH - HO
Error: Could not find angle parameter: CA - N2 - OHBuilding proper torsion parameters.
Error: ** No torsion terms for H-N2-OH-HO
Error: ** No torsion terms for CA-N2-OH-HOBuilding improper torsion parameters. ** Warning: No sp2 improper torsion term for CT-H-NT-CT atoms are: C5 H3 N3 C2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA atoms are: CG CE2 CD2 CE3 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB atoms are: NE1 CZ2 CE2 CD2 total 834 improper torsions appliedBuilding H-Bond parameters.Incorporating Non-Bonded adjustments.
Warning: Parameter file was not saved.> quit Quit
Exiting LEaP: Errors = 6; Warnings = 1; Notes = 0.
Any suggestion will be highly appreciated!
Thanks,Sarah
On Friday, 28 August 2020, 02:03:37 BST, David A Case <david.case.rutgers.edu> wrote:
On Thu, Aug 27, 2020, Sarah Jane wrote:
>
> Here is the antechamber command:antechamber -fi pdb -i HAR.pdb -fo mol2 -o
> HAR.mol2 -c bcc -nc 0 -at amber -s 2 -dr no
You HAR.pdb file has a very bad placement of the HO1 atom: it is only
1.6 Å from the CZ atom. I'm guessing that this is confusing to
antechamber, although the C=N double bond *could* be a problem.
Try rotating the HO1 above to point away from the rest of the molecule.
You also have mulitple unsatisfied valencies at the C and N atoms:
antechamber expects a complete moledule, not just an amino acid
fragment. You need to put capping groups on, run antehcamber, then take
the capping groups off.
Try this: go to http://ambermd.org/antechamber/, click on "tutorials and
examples", then on "generate residue topology files for non-standard
amino acids". (Apologies if you have already done this.....)
...good luck...dac
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Received on Sun Sep 27 2020 - 17:30:02 PDT
