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

[Mark Abraham]

nikhil damle wrote:
> OK till here done ! the pdb file generated for EM should have ATP 
> molecule @proper position as input .top file has the ATP.itp included. 
> It did not have. If I do -ci it would randomly replace the solvent. I 
> want ATP @ its proper location. how do i do this ?

Like I implied several emails ago, you should order the [molecules] 
entries according to the coordinate file, as normal.

Mark