 |
 |
Hi all! Apologies about this post in advance because I know there have been multiple posts about this issue previously. I am working with ccpnAnalysis 2.3.1 / ARIA 2.3 calculation on an N-acetylated and C-amidated peptide. ARIA just seems to not recognize the Acy and Nh3 residues. I followed Piotr Wysoczanski's earlier post at https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1105&L=CCPNMR&P=R7525&1=CCPNMR&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 So based on what he suggested, I tried to change "other" to "protein" inside the ccpnAnalysis project tree (/project/memops/Implementation/), put them in one fragment (/project/ccp/molecule/MolSystem), copied the Acy.xml and Nh3.xml file from /ccpnmr/ccpnmr2.3/data/ccp/molecule/ChemComp/ to /project/ccp/molecular/ChemComp/, and modified all the files in aria to include naming/parameters of Acy/Nh3. That didn't work. Then I changed the original Acy.xml and Nh3.xml files in /ccpnmr/ccpnmr2.3/data/ccp/molecule/ChemComp/ to "protein", and created a new project, which didn't work either. The error message from ARIA generate.out is pasted at the end of this message. I am not sure where the problem is located and how to solve this. It could also be errors about the ARIA file I edited in order to incorporate non standard amino acids (AminoAcid.py, atomnames.xml, iupac.xml, Nomenclature.py, PseudoAtom.py, parallhdg5.3.pro, topallhdg5.3.pro). I would really appreciate any comments and suggestions! Bests, Yuan Yang %GENRES-ERR: residue not found in topology file %PATCH-ERR: to be deleted bond -C +N not found in molecular structure. %PATCH-ERR: to be deleted angle -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted angle -O -C +N not found in molecular structure. %PATCH-ERR: to be deleted angle -C +N +CA not found in molecular structure. %PATCH-ERR: to be deleted angle -C +N +HN not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C -O not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C -O not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C -O not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C -O not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C -O not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C -O not found in molecular structure. %PATCH-ERR: to be deleted improper -C -CA +N -O not found in molecular structure. %PATCH-ERR: to be deleted improper +N -C +CA +HN not found in molecular structure. %PATCH-ERR: to be deleted improper -CA -C +N +CA not found in molecular structure. %GENRES-ERR: residue not found in topology file %PATCH-ERR: to be deleted bond -C +N not found in molecular structure. %PATCH-ERR: to be deleted angle -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted angle -O -C +N not found in molecular structure. %PATCH-ERR: to be deleted angle -C +N +CA not found in molecular structure. %PATCH-ERR: to be deleted angle -C +N +HN not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +C not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -C +N +CA +CB not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted dihedral -CB -CA -C +N not found in molecular structure. %PATCH-ERR: to be deleted improper -C -CA +N -O not found in molecular structure. %PATCH-ERR: to be deleted improper +N -C +CA +HN not found in molecular structure. %PATCH-ERR: to be deleted improper -CA -C +N +CA not found in molecular structure.