nikhil damle wrote:
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.
pdb2gmx only writes a single [moleculetype] section, plus possibly
solvent, so it will not cope as you would wish with a coordinate file
with protein and free ATP.
The format of a molecule .itp file is a subset of that for a .top file,
so you can feed a separate coordinate file containing only ATP to
pdb2gmx to get that .top file. Remove the inappropriate header and
footer sections, and then #include this new .itp file in your original
.top file appropriately, and adjust its [molecules] section correctly.
Mark
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