[gmx-users] Required help in topology making

supti mukherjee suptimukherjee at gmail.com
Wed Jul 29 08:45:31 CEST 2009

Dear All
   I have a protein where one residue ( Lysine ) is making a covalent bond
   the cofactor Pyridoxal phosphate. I have created other parameters of
   heteroatom PLP  through PRODRG and manual checking. But I am not sure how
   include the parameters for the "imine" bond ( C=N  bond ) that has been
   formed between side chain amine group of lysine and aldehyde group of
   Pyridoxal phosphate.
   Do I have to edit  C-termini database file ( ff????-c.tdb ) ?
   A clue to this problem will be highly appreciated.
   Supti Mukhopadhyay
   Senior Research Fellow
   Department of Psychopharmacology
   NIMHANS, Bangalore
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