Dear all,
I am trying to generate a topology file for GTP and GDP using ATB. When doing so, I selected the option "United Atom". However, the output files (*.itp and *.pdb) contain some hydrogen atoms connected to carbons in the aromatic rings and in the sugar. (see below a fragment of GDP's itp file) Why these hydrogen atoms are appearing?
Another point is related with the hydrogens bonded to the oxygen atoms of the phosphate groups, Can I get a topology file without these hydrogen atoms?
Thanks for the help!
At the end I did not use ATB. Instead I modified the aminoacids.rtp file of GROMOS43a1 to include GTP and GDP from the existent data of ATP (the sugar and the phosphate groups) and DGUA (the nitrogenous base). It turned to be easier than with ATB and I could set with which H atoms I would work,
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