AMBER Archive (2006)

Subject: AMBER: problem with saving the parameters file

From: amere swathi (swathia77_at_yahoo.com)
Date: Wed Jul 05 2006 - 03:50:40 CDT

hai,
  I have solvated the protein using TIP3PBOX 8 2. When I try to save the topology and coordinates file ( .top and .rec) using the following command
   
>saveamberparm prot rec.top rec.crd
   
  the files are not being saved with the following error message.
   
  could not find angle parameter: N-CT-N
  could not find angle parameter: N-CT-N
  could not find angle parameter: N-CT-N
  could not find angle parameter: N-CT-N
  building proper torsion parmeters
   
  1-4: ang 5-9 duplicates bond ('triangular' bond) or angle ('square' bond)
  1-4: ang 2-7 duplicates bond ('triangular' bond) or angle ('square' bond)
  building imroper torsion parameters
  total 708 improper torsions applied
  building H bond parameters
  parameter file was not saved.
   
  Can anyone help me to properly save the .top and .rec with out these messages.
   
  Thanking you in advance.
   
  reagrds,
  swathi

                                 
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