[gmx-users] simulation of protein in presence of ATP
Mark.Abraham at anu.edu.au
Mon Jun 22 06:57:24 CEST 2009
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.
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