Hi, Kamali,
I haven't tried Dan's or Robin's method but will likely do so soon enough.
I'm not sure why you're using addions2 or why you're adding ions before
solvating the system. My responses, inserted below, assume all you care
about is that you end up with 0.15 M salt and that the initial
configuration of ions is evenly distributed around your system.
On Fri, Jun 22, 2012 at 2:51 PM, Kamali Sripathi <ksripath.umich.edu> wrote:
> Thanks a lot, Robin; I'll give that a try.
>
> Dr. Cheatham, I actually had a follow-up question for you. I've been using
> your molarity.perl script to calculate the number of ions I'd need for a
> certain box size. My problem is that I solvate after adding ions, so that
> the box size is always a bit off. For example, I calculated by hand (before
> I had found the script) that I needed 111 molecules of KCl to reach a
> concentration of 0.15 M. Just to double-check, I plugged in my box
> dimensions after adding these 111 molecules and solvated my system. The
> script then told me that I'd need 128 molecules. I started over, and added
> 128 molecules to my system and solvated. As another double-check, I plugged
> in the parameters of this box into the molarity.perl script, which told me
> that I now needed 131 molecules. I know the best way to do this would be to
> solvate my system and use addions2 to add molecules after solvation.
> However (as I think I mentioned), I tried this, and my system is so big
> that Leap crashed.
Did you try adding ions one pair at a time (as Tom suggested)? Did you try
using addions instead of addions2 (see AmberTools15 manual page 52) or
Robin's AddIonsRand?
> Do you have any suggestions for how I might get my
> desired salt concentration?
>
In case a future Google search is made that this thread comes up on:
*Step 1.* Run leap with the final solvent size you want. Do not add any
ions yet. Just solvent.
*Step 2.* Use *tail* (see bash, please) to get the box information (last
line of *crd file), e.g.,
96.1984 97.1984 98.1984 109.4712190 109.4712190 109.4712190
*Step 3.* Copy and paste the box information into Professor Tom's script
appropriately, e.g.,
./Tom.pl *0.15* 96.1984 97.1984 98.1984 109.4712190 109.4712190 109.4712190
Resulting in,
MOLARITY = 0.150
Box size = 96.198 97.198 98.198 109.471 109.471 109.471
Volume = 706821.110
63.847 molecules are necessary to make a molarity of 0.15M
*Step 4. Bash a bit,*
#!/bin/bash
for i in $(seq 1 64); do
echo addions mol K+ 1 Cl- 1
done
Resulting in 64 lines of,
addions mol K+ 1 Cl- 1
*Step 4.1* Add the 64 lines of "addions mol K+ 1 Cl-" to the leap
script *_*after
solvate line_**, e.g.
#!/bin/bash
#leap stuff here
mol = loadpdb ./solute.pdb
...
*solvateOCT mol TIP3PBOX 84*
*addions mol K+ 0*
*addions mol K+ 1 Cl- 1*
...
...
*Step 4.2. Run your leap script like so,*
./leap_script.sh .& leap_script.out-2012-06.22.log &
then you can
grep "Done adding ions" leap_script.out-2012-06.22.log|wc
to see how far along leap is, if you're impatient and in need of instant
gratification.
*Step 5. Randomize your ions. *This step ought to address your second issue
of ions hanging around some domains and not others.
ptraj prmtop << EOF
trajin inpcrd
trajout inpcrd.rand restart
prnlev 3
randomizeions :K+,Cl- around :$X by Y overlap Z noimage
EOF
Where X= the resnames of all the residues in the solute, to suit; Y and Z
can be found in the literature. Professor Tom has some very detailed
Methods sections 8^)
Things to consider: adding net neutralizing ions; box size after
equilibration; whether you really want ions to be randomized or you want
them to go where the electrostatics are good. For this you may want to look
into Dan's work. Also, Robin's method is probably not only easier but
faster than what I've outlined here...
HTH,
Kevin
--
-- - -
HK
-----------------------------------------------------------------------------
Kevin Hauser
The Louis and Beatrice Laufer
Center for Physical and Quantitative Biology
at Stony Brook University
National Institutes of Health,
Chemical Biology Interface Training Program Fellow
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
Phone: (561) 635.1848
Email: 84hauser.gmail.com
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Received on Fri Jun 22 2012 - 14:00:04 PDT
