Dear Jason,
Thank you for your kind support and useful advice.
I solve the problem by using your excellent program, "parmed".
It help me to achieve the aim, more quickly and accurately.
I can perform the simulations I intended.
By the way, I have another problem in terms of SHAKE when I performed
simulations
With the modified prmtop.
As you know, I set pseudo bonds between atoms in protein and ions.
Then, ions bonds with hydrogen, too. These cause anomalous geometry,
thus stopping simulation.
To avoid such a problem,
I edited "FLAG BONDS_INC_HYDROGEN" and "FLAG BONDS_WITHOUT_HYDROGEN",
where ion-hydrogen bond pairs were moved from the former to the later.
However, it does not work; sander cannot access these additionally modified
prmtop file.
In fact, simulations were stopped by showing
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
at the last line of mdout.
Additionally, "ambpdb" did not work, too.
Then I guess such an additional modification break a PRMTOP format...
If it cannot be solved easily,
I set SHAKE off in simulations.
But If you have some idea to solve this problem,
I am most grateful to hear that.
Yours sincerely,
Ikuo KURISAKI
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, June 10, 2013 10:01 PM
To: AMBER Mailing List
Cc: AMBER Mailing List
Subject: Re: [AMBER] How to make a specific non-bonded interaction off
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 Thu Jun 13 2013 - 20:30:02 PDT
