VMD-L Mailing List

From: Rima Chaudhuri (rima_chau_at_yahoo.com)
Date: Thu Mar 23 2006 - 20:20:10 CST

Hi,
   
  I am trying to generate a psf file of a protein with 3 chains. On following the tutorial instructions of using the command 'segment U ....' it just choses one of the chains(but I want it to read all the 3 chains), moreover it gives an error for every residue that it reads from the pdb file. On loading the resuting psf and pdb files that i creates, there are astray residues far off from the protein chain (last 2 residues).
  If I use just 1 chain as the input pdb file, it does not give any error but on trying to set coordinates via command:
  coordpdb sarsp_A.pdb U
  It gives the following error.
  Warning: failed to set coordinate for atom CG2 VAL:301 U for every residue respectively.
   
  Please let me know :
  1)what needs to be done if I want to use all 3 chains
  2)how to get rid of these errors.
   
  Thanks
  -Rima

                
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