Hello Bill Ross,
Thank you for your response and the suggestions.
However, if I am going to the AMBER tutorial-3 regarding the MM-PBSA
calculation, I can see the use of gas phase topology (prmtop) files in the
extracts_coords.mmpbsa and binding_energy.mmpbsa files with the use of
"ras-raf_solvated.prmtop"
to generate the trajectory files.
Also, I wonder how these works in the tutorial. I am a bit confused with
this. If I am wrong, rectify me.
Does your trajectory files (prod_1.mdcrd, prod_2.mdcrd...) contain water
molecules ?
I just wanted to calculate the binding free energy between the
protein-ligand complex of a solvated system. Please do suggest me the right
path.
Thanks
Siddharth
On Fri, Sep 3, 2010 at 8:14 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > FATAL: NATOM mismatch in coord and topology files.
>
> The prmtop for a solvated system cannot be used with crds for the vacuum
> version and vice-versa.
>
> Bill
>
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--
Siddharth Rastogi
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Received on Wed Sep 08 2010 - 18:00:03 PDT
