Thanks for your answer, Dr. Cheatham. I've actually been using your script
to calculate molarity; it's been really helpful!
I actually found, through a discussion with my collaborators, that I was
probably using the wrong ion parameters. I was just using the default AMBER
parameters, but yesterday I submitted for equilibration a new structure
using the K+ and Cl- parameters from Joung and Cheatham, 2008. I am hoping
this will correct the problem.
Actually, now that I think of it, ptraj didn't actually crash when I tired
the randomizeions command; it was just taking so long and I wanted my
processors to do other things, so I forced it to quit.
Thanks again, and have a great day,
Kamali
On Tue, Jun 19, 2012 at 9:16 AM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > I'm trying to simulate an 800+ protein-RNA complex with a physiological
> > concentration of 0.15 M KCl. During my first try to add ions and solvate
> > the system, I added ions first and then solvated the system. However,
> > during equilibration, I believe that this resulted in un-physiological
> > "clumps" of KCl. As I saw in the AMBER mailing list archive, I tried to
>
> ...although it is slow, I add ions one at a time and this tends to avoid
> the problems with LEaP clumping ions or putting them in a long linear
> chain...
>
> addions UNIT K+ 0
> addions UNIT Cl- 0
>
> addions UNIT K+ 1 Cl- 1
> addions UNIT K+ 1 Cl- 1
> addions UNIT K+ 1 Cl- 1
> addions UNIT K+ 1 Cl- 1
> addions UNIT K+ 1 Cl- 1
> ...
>
> To "estimate" molarity, I use a simple Perl script below.
>
> perl ~/molarity.perl 0.15 84.02 84.02 84.02 90.0 90.0 90.0
> # ^ X Y Z alpha beta gamma
> # molarity M
>
> > system was so big that Leap crashed. A similar situation occurred when I
> > tried to use the ptraj randomizeions command. Does anyone know of a way
>
> randomizeions in ptraj should randomly swap with water; did it lead to
> clumping or simply an error / core dump?
>
> --tec3
>
> ----------------
>
> #!/usr/sbin/perl
>
> $molar = $ARGV[0];
> $box_x = $ARGV[1];
> $box_y = $ARGV[2];
> $box_z = $ARGV[3];
> $box_a = $ARGV[4];
> $box_b = $ARGV[5];
> $box_g = $ARGV[6];
>
>
> if ($box_x == 0) {
> printf("Usage: molarity box-x box-y box-z alpha beta gamma\n");
> die;
> }
>
> if ($box_y == 0) {
> $box_y = $box_x;
> }
>
> if ($box_z == 0) {
> $box_z = $box_x;
> }
>
> if ($box_a == 0) {
> $box_a = 90.0;
> }
>
> if ($box_b == 0) {
> $box_b = $box_a;
> }
>
> if ($box_g == 0) {
> $box_g = $box_a;
> }
>
> $torad = 2 * 3.141592654 / 360.0;
>
> $rad_a = $box_a * $torad;
> $rad_b = $box_b * $torad;
> $rad_g = $box_g * $torad;
>
> $angles = 1 - cos($rad_a)*cos($rad_a) - cos($rad_b)*cos($rad_b) -
> cos($rad_g)*cos($rad_g);
> $angles += 2 * cos($rad_a)*cos($rad_b)*cos($rad_g);
> $angles = sqrt($angles);
>
>
> $volume = $box_x * $box_y * $box_z * $angles;
>
>
> $molecules = 6.022 * $volume * $molar / 10000;
>
> printf(" MOLARITY = %8.3f\n", $molar);
> printf(" Box size = %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", $box_x,
> $box_y, $box_z, $box_a, $box_b, $box_g);
> printf(" Volume = %8.3f\n", $volume);
> printf("\n %8.3f molecules are necessary to make a molarity of %6.2f
> M\n\n", $molecules, $molar);
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
--
Kamali Sripathi
Graduate Student, Medicinal Chemistry
Walter Laboratory
930 North University
Ann Arbor, MI, 48109
ksripath.umich.edu
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Received on Tue Jun 19 2012 - 08:00:03 PDT
