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.
Regards,
Nikhil
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