Re: [AMBER] Fwd: CPPTRAJ trajout results "weird" pdb

From: David A Case <>
Date: Thu, 19 Mar 2015 08:03:07 -0400

On Thu, Mar 19, 2015, Chinh Su Tran To wrote:
> I used cpptraj to convert a trajectory frame into pdb format, but I got
> very "weird" pdb file (Sorry, I cannot attach it here as it is more than
> 5Mb and the post was bounced back). When I visualized it, it gave me a
> "flat" structure with clashes (image attached).
> Could you please help comment if I missed something? Thanks.

This may be a problem with your visualization(?) Your pdb file will have 2500
"models" (separate frames), but it may be that your visualization program
doesn't handle this correctly. Or, it may be that the CRYST1 record for
the truncated octahedron is with wrong, or is being misinterpreted by your
visualization program.

Start by just saving one frame the pdb file: that will be small enough that
you can post it.


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Received on Thu Mar 19 2015 - 05:30:02 PDT
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