Chimera doesn't display AMBER molecular dynamics trajectories with periodic boundary condition.
Hi, I'm using chimera 1.2309 version. And I found out that MD movie module in chimera doesn't display AMBER trajectory file with periodic condition correctly. I works well only with non-periodic condition trajectory file. Another visualization program, VMD, has two seperated options for AMBER trajectory file: with periodic condition and not. I prefer display style of chimera. So, I really hope to see my AMBER trajectory with Chimera. Do you have any tips for this problem? or have plan to add the format, with periodic boundary condition. :-) Thanks again for your great program and have a nice day! ============================================= Lee, juyong Ph.D student, Department of chemistry, Seoul National University, Korea. drfaust23@gmail.com
On Jan 11, 2007, at 12:26 AM, juyong Lee wrote:
Hi, I'm using chimera 1.2309 version.
And I found out that MD movie module in chimera doesn't display AMBER trajectory file with periodic condition correctly.
I works well only with non-periodic condition trajectory file.
Are you saying that trying to show such a trajectory gives you an error, or that it just doesn't look correct? Chimera should show Amber periodic-boundary trajectories without problem. Now, a periodic-boundary simulation may look wrong as solvent drifts out of the center box. If this is the problem, you would need to use ptraj's "image" command to re-image the solvent into the solute box.
Another visualization program, VMD, has two seperated options for AMBER trajectory file: with periodic condition and not.
VMD can't automatically determine whether a trajectory is PBC or not, whereas Chimera can -- that's why VMD has separate options.
I prefer display style of chimera. So, I really hope to see my AMBER trajectory with Chimera.
Do you have any tips for this problem? or have plan to add the format, with periodic boundary condition. :-)
If you are actually getting an error, or if you are already re- imaging your solvent and things still don't look right then if you send me a trajectory that exhibits the problem I will investigate. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
On a related note, there _is_ an error in the way Chimera handles NAMD/CHARMm DCD files _without_ periodic box information in the 1.2304-1.2318 releases. You will get a "DCD format error 9". If this bites you, send me mail and I'll send you a file with the fix that you can drop into your Chimera. --Eric On Jan 11, 2007, at 12:26 AM, juyong Lee wrote:
Hi, I'm using chimera 1.2309 version.
And I found out that MD movie module in chimera doesn't display AMBER trajectory file with periodic condition correctly.
I works well only with non-periodic condition trajectory file.
Another visualization program, VMD, has two seperated options for AMBER trajectory file: with periodic condition and not.
I prefer display style of chimera. So, I really hope to see my AMBER trajectory with Chimera.
Do you have any tips for this problem? or have plan to add the format, with periodic boundary condition. :-)
Thanks again for your great program and have a nice day!
============================================= Lee, juyong Ph.D student, Department of chemistry, Seoul National University, Korea. drfaust23@gmail.com
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participants (2)
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Eric Pettersen -
juyong Lee