Hello, I am having issues with creating input files for a calcium dependant cysteine protease (PDB entry 3DF0). The original PDB file contained 3 chains, and I have completely deleted chain C which was the co-crystallised ligand as well as all waters. Calcium ions have not been removed. The PDB was then put through VMD to remove all protons as per the usual set up. However, when the file was loaded into tleap using ff99SB to create the input files, the following error messages occurred.
FATAL: Atom .R<ILE 25>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 73>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 81>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 88>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 89>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 97>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 111>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 120>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 138>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 188>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 211>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 227>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 228>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 242>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 244>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 282>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 284>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 340>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 389>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 412>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 429>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 433>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 446>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 466>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 499>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 516>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 520>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 523>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 530>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 548>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 556>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 567>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 574>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 579>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 599>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 604>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 610>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 614>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 646>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 656>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 657>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 671>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 675>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 687>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 692>.A<CD 20> does not have a type.
FATAL: Atom .R<CGLY 701>.A<OCT1 9> does not have a type.
FATAL: Atom .R<CGLY 701>.A<OCT2 10> does not have a type.
FATAL: Atom .R<ILE 730>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 748>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 778>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 784>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 796>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 816>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 820>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 821>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 837>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 861>.A<CD 20> does not have a type.
FATAL: Atom .R<ILE 865>.A<CD 20> does not have a type.
FATAL: Atom .R<CSER 875>.A<OCT1 13> does not have a type.
FATAL: Atom .R<CSER 875>.A<OCT2 14> does not have a type.
FATAL: Atom .R<CA 876>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 877>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 878>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 879>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 880>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 881>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 882>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 883>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 884>.A<CA 1> does not have a type.
FATAL: Atom .R<CA 885>.A<CA 1> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Is there anyone able to help me solve this issue so that the forcefield is able to recognise this particular class of atom as well as removing the large amount of close contacts? Ideally I would like to keep the calcium ions in the file as they are an important factor in the protein's activation.
Thank you for your time.
Regards,
Theo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 30 2013 - 18:00:03 PDT
