On Jun 10, 2013, at 6:22 AM, "kurisaki" <kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Amber Developer,
>
> I'm just trying to ignore specific non-bonded interactions,
> e.g. a set of atoms in protein vs an ion molecules.
>
> To achieve the purpose,
> I modify "%FLAG NUMBER_EXCLUDED_ATOMS" and "%FLAG EXCLUDED_ATOMS_LIST"
> in PRMTOP file but It does not work at all, thus giving same energy.
The PME nonbonded code ignores these sections of the prmtop file and recomputes this list based on the bonds angles and dihedrals present in the system.
That said, giving details about exactly how you modified the topology file will help us aid you in debugging your problems. ParmEd has an addExclusions command that let's you do this 'correctly' (although as I mentioned it only works for GB simulations). Once you start modifying the prmtop, the already non-existent warranty for amber is voided. Given the complexity of the file, the only prmtop modifications I would consider trusting to have been done correctly are those done by a program that we release and have experience with (e.g., parmed or cpptraj)
>
> I'd like to know how I can make a specific non-bond interaction off.
With parmed you can do this easily with vdW terms by using changeLJPair. To do the same for nonbonded interactions in explicit solvent, you would either need to change the code or add a bond between every pair of atoms you want excluded using ParmEd with a 0 force constant using the setBond command (I've never tried this so I cannot guarantee anything, but I think it should work).
>
> Yours sincerely,
>
> Ikuo KURISAKI
>
> PS
>
> Let's assume that I make off protein-ion interaction.
> When I tried t modify a PRMTOP file,
> I added the ion's atom number to components of excluded atom list
> associated with protein.
> Components of number excluded atoms were also modified
> Corresponding to the above modification.
This is not enough. You also need to adjust the POINTERS section accordingly. And it's important to know the idiosyncrasies of the exclusion list, like each exclusion is listed only once for the lower index atom and atoms with no exclusions are excluded from atom 0. As I mentioned, prmtops are too complex to do non-trivial modifications by hand. It is a moot point anyway since the PME code ignores these sections.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 10 2013 - 06:30:02 PDT
