[gmx-users] simulation of protein in presence of ATP

nikhil damle pdnikhil at yahoo.co.in
Mon Jun 22 06:39:20 CEST 2009

Hi all,
       I want to carry out a MD simulation of a receptor protein in presence of ATP molecule. ATP is included in .rtp file of ffG43a1 force field. but  post pdb2gmx, .pdb output file does not show crds of ATP. Does it mean that ATP is not recognized as a residue of protein in spite of being included in .rtp file. If so how does one carry out this simulation ? If .itp file of ATP is an option, how can one get the specific values of charges etc for constructing .itp file. Manual does not mention anything regarding it. 

      Please help as soon as possible.


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