VMD-L Mailing List

From: Shubhadip Das (d.shubhadip_at_yahoo.com)
Date: Sat Dec 01 2012 - 01:49:23 CST

Dear VMD-L User, I have a pdb file of a protein which has residue name "MOL" for each residue. When I tried to load its graphical representation in cartoon option the following lines appears in window.Will you please let me know how should I proceed to avoid this problem. Info) Determining bond structure from distance search ... Info) Analyzing structure ... Info)    Atoms: 147 Info)    Bonds: 150 Info)    Angles: 0  Dihedrals: 0  Impropers: 0  Cross-terms: 0 Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0 Info)    Residues: 1 Info)    Waters: 0 Info)    Segments: 1 Info)    Fragments: 1   Protein: 0   Nucleic: 0 Info) In any publication of scientific results based in part or Info) completely on the use of the program STRIDE, please reference: Info)  Frishman,D & Argos,P. (1995) Knowledge-based secondary structure Info)  assignment. Proteins: structure, function and genetics, 23, 566-579. Error reading PDB file /tmp/fileLRrl7d ERROR) Unable to find Stride output file: /tmp/fileoIA3rD ERROR) Stride::read_stride_record: unable to read output file from Stride ERROR) Call to Stride program failed. Info) VMD for LINUX, version 1.9.1 (February 1, 2012) Info) Exiting normally. Thanking you in advance Sincerely, Shubhadip Das Research Scholar IIT Guwahati India