Thanks Jason!
I should have figured it wouldn't be all that easy to manually edit the
prmtop.
Yes, you did sent me parmed, thanks! I looked through the information of
how to use it, and had a project student (for whose project this is) try it
out. She used the following input (addexclusions.in):
#Add exclusions to the exclusion list so that non-bonded interactions
between mask1 and mask2 atoms are not computed.
addExclusions :Na+ :Na+,Cl-
addExclusions :Cl- :Na+,Cl-
parmout exclusions2.prmtop
And then ran parmed.py:
parmed.py 4ions.prmtop addexclusions.in
When I run minimization with the resulting exclusions2.prmtop, the energies
are again identical as without the exclusions.
It would be great if you could tell me what is wrong with how we are trying
to use the addExclusions command.
Thanks,
Marc
On 6 December 2011 17:03, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Dec 6, 2011 at 11:15 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> > wrote:
> >
> >
> > 4ions.prmtop is attached.
> > I created a modified version (i.e. with all ion-ion pairs in the
> exclusion
> > list): 4ions_ex.prmtop (attached)
> >
> > $ diff 4ions.prmtop 4ions_ex.prmtop
> > 25c25
> > < 1 1 1 1
> > ---
> > > 3 3 3 3
> > 91c91,92
> > < 0 0 0 0
> > ---
> > > 2 3 4 1 3 4 1 2
> 4
> > 1
> > > 2 3
> >
>
> These modifications are not correct (and incomplete). Modifying the
> topology file generally entails more than you'd expect. You have to adjust
> the appropriate pointer in the POINTERS section as well as make sure that
> the format (and potentially ordering) of the various sections are
> consistent with what sander/pmemd expect. My general warning here is:
> understanding the topology file is difficult, but successfully modifying
> the topology file (in a non-trivial way) is an order of magnitude more
> difficult, something I dare not do by hand even after studying the prmtop
> format and the sander/pmemd code that uses it.
>
> Did you try using parmed or xparmed to do this? (I can't remember if I
> sent you the code for it). When I create a 4-Na+ system and use parmed to
> add every atom to each others' exclusion list, I get the appropriate result
> of 0s for every energy value (since no nonbonded interactions are
> calculated and none of the atoms are bonded with one another), and I get
> the "appropriate" energies for the original topology.
>
> If you need parmed or xparmed, just let me know and I'll send it to you, or
> if you need instructions on how to use it, I can provide those as well.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Dec 06 2011 - 09:30:04 PST
