Hi Jason,
Yes, I think the student originally put them in one command, but played
around as it didn't seem to work.
I get the same prmtop (only timestamp differs) when I do use the combined
command, and the correct atoms (all 4 ions) are selected by the mask.
I've attached:
4ions.prmtop original prmtop
exclusions2.prmtop prmtop modified by parmed.py (addexclusions.in)
addexclusions.out the output from parmed, including the results
from "printDetails :Na+,Cl-"
Thanks in advance for your help!
Marc
PS I note that exclusions2.prmtop is a lot smaller than the original
4ions.prmtop, but I don't think this is the problem
On 6 December 2011 19:50, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Dec 6, 2011 at 12:16 PM, Marc van der Kamp <
> marcvanderkamp.gmail.com
> > wrote:
>
> > 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-
> >
>
> You could combine these 2 into
>
> addExclusions :Na+,Cl- :Na+,Cl-
>
> It would be helpful to put the command "printDetails :Na+,Cl-" to see what
> atoms are selected by the masks.
>
> Also, can you send me the 2 topology files? (exclusions2.prmtop and the
> original) so I can compare them? This was the same command I used
> successfully in the email I sent above.
>
> Thanks!
> 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 - 13:00:02 PST
