Thank you so much, Brian.
The values should be at the end of crd files.
Best,
Ren
-----Original Message-----
From: Brian Radak [mailto:radak004.umn.edu]
Sent: Wednesday, August 08, 2012 2:26 PM
To: AMBER Mailing List
Subject: Re: [AMBER] how to make a certain ionic concentration for the system?
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 FORTUNE(r) Magazine's
> "100 Best Companies to Work For(r)" list seven years in a row. Designated as
> a Magnet hospital for excellence in nursing. Visit us at
> methodisthealth.com. Follow us at twitter.com/MethodistHosp and
> www.facebook.com/MethodistHospital. ***CONFIDENTIALITY NOTICE*** This
> e-mail is the property of The Methodist Hospital and/or its relevant
> affiliates and may contain restricted and privileged material for the sole
> use of the intended recipient(s). Any review, use, distribution or
> disclosure by others is strictly prohibited. If you are not the intended
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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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Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list seven years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at methodisthealth.com. Follow us at twitter.com/MethodistHosp and www.facebook.com/MethodistHospital.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
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Received on Thu Aug 09 2012 - 10:00:04 PDT
