AMBER Archive (2008)

Subject: Re: AMBER: coordinate file question

From: Robert Hanson (hansonr_at_stolaf.edu)
Date: Tue Sep 30 2008 - 12:24:47 CDT

thanks, this seems to be working great.

On Tue, Sep 30, 2008 at 8:55 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Robert,
>
>
>
> Yes the IFBOX in the prmtop should tell you whether to look for the box or
> not - other programs like VMD just have two input formats to choose from -
> AMBER Coordinates and AMBER Coordinates with Box.
>
>
>
> Good luck,
>
> Ross
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Robert Hanson
> *Sent:* Tuesday, September 30, 2008 6:30 AM
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: coordinate file question
>
>
>
> Thanks, Ross,
>
> Great. That seems to work now.
>
> To be clear: It's the IFBOX parameter = 1 that determines that? (Files from
> some sources I see do not have that extra point.) So if IFBOX == 0, then I
> should not have the box size?
>
> Bob
>
> On Mon, Sep 29, 2008 at 10:33 PM, Ross Walker <ross_at_rosswalker.co.uk>
> wrote:
>
> Hi Robert,
>
>
>
> The last coordinate is the box dimensions. Coordinate files come in
> multiple flavors.
>
>
>
> 1) inpcrd file
>
>
>
> Gas phase - should contain 3*natom
>
> Orthorhombic periodic - should contain 3*natom +
> xbox,ybox,zbox,alpha,beta,gamma
>
> where alpha,beta,gamma = 90.0
>
> truncated octahedral periodic - should contain 3*natom +
> xbox,ybox,zbox,alpha,beta,gamma
>
>
>
> 2) restart file. As inpcrd file but contains 3*natom + 3*velocity +
> box.....
>
>
>
> 3) mdcrd file (fomatted) - 3*natom + xbox,ybox,zbox
>
>
>
> 4) mdcrd file (netcdf binary) - see http://ambermd.org/netcdf/nctraj.html
>
>
>
> Also see http://ambermd.org/formats.html
>
>
>
> All the best
>
> Ross
>
>
>
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Robert Hanson
> *Sent:* Monday, September 29, 2008 8:16 PM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: coordinate file question
>
>
>
> I'm setting up Jmol to read Amber topology / coordinate files. But I've run
> into an odd snag. It seems the coordinate files that I have has one too many
> coordinates. I'll send links to the files if necessary, but does it make
> sense that a topology file reading
>
> %FLAG
> POINTERS
> %FORMAT(10I8)
>
> 37300 16 29669 6234 12927 6917 28267 6499
> 0 0
> 87674 9013 6234 6917 6499 47 101 41
> 31 1
> 0 0 0 0 0 0 0 1
> 24 0
> 0
>
> has a coordinate file that contains blocks of 37301 * 3 coordinates?
> Does the last coordinate somehow mean something other than an atom? Do
> these parameters somehow indicate that an additional coordinate is present?
>
> Thanks,
>
> Bob Hanson
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> 

-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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