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

[Mark Abraham]

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