[AMBER] ptraj

From: Steve Seibold <seibold.chemistry.msu.edu>
Date: Mon, 12 Jul 2010 12:52:07 -0400

Hello Amber
I have fixed the problem of xleap now, but have a problem with ptraj that has worsened since I recompiled with appropriate libraries. The problem is:

I take my large protein system trajectories that work well with amber8 and attempt to use amber11 ptraj on a single, non-combined mdcrd file to measure distances, I get "segmentation fault" and distances are thus, not given.

When I use amber11 ptraj with multiple, non-combined mdcrd files, it starts out fine and reads all sets from separate mdcrd files correctly. It then starts to "processing amber trajectory file.mdcrd and some it reads, but always fails with a segmentation fault at the last mdcrd file.

Now, if I take a small protein system's trajectories that works with amber8 and attempt to use amber11 ptraj on a single OR combined mdcrd file every thing works fine.

So, is there a size limitation in amber11 AmberTools ptraj??

Sander does not appear to have a problem with my large system as it appears to be running fine.

Thanks for your help.

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Received on Mon Jul 12 2010 - 10:00:06 PDT
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