Hi Ren,
The values are in the crd and rst file, as well as the prmtop file
(although I don't believe these are used anymore?). Check out the AMBER
file formats page:
http://ambermd.org/formats.html
If there is a box it's parameters will be the format "a b c alpha beta
gamma".
Regards,
Brian
On Wed, Aug 8, 2012 at 12:29 PM, Kong, Ren <rkong.tmhs.org> wrote:
> Hi Amber users,
>
> I'm trying to add ions to make a certain ionic concentration for my
> system, like 0.15 mol/L KCL.
> And I search in the mail list and find Thomas Cheatham III's script:
>
> --tec3
>
>
> molarity.perl
>
> #!/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);
>
> I'm wondering how to get the x,y,z and alpha, beta, gamma value?
> I reviewed the leap.log files and not sure about what these value are.
>
> Does anyone use this scrip to count the ion number?
>
> Thanks a lot.
>
> Ren Kong Ph.D.
>
> Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of
> America's "Best Hospitals" in 13 specialties. Named to FORTUNEŽ Magazine's
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Wed Aug 08 2012 - 12:30:02 PDT
