[AMBER] Tutorial B1 problems

From: Jennifer L. Muzyka <jennifer.muzyka.centre.edu>
Date: Mon, 2 Jul 2018 15:46:58 +0000

We are working through Tutorial B1: Simulating a small fragment of DNA and are struggling with section 3 (http://ambermd.org/tutorials/basic/tutorial1/section3.htm).

The sander output files look fine in xmgrace. But when we open the files in VMD, we get the error message shown below.

Info) Using plugin crd for coordinates from file /Users/daniel.thompson/Desktop/AMBERtest/polyAT_vac_md1_12Acut.mdcrd

Problem reading CRD file

Info) Finished with coordinate file /Users/daniel.thompson/Desktop/AMBERtest/polyAT_vac_md1_12Acut.mdcrd.

So then we tried to download the known output files from the tutorial for comparison purposes. Unfortunately the output files http://ambermd.org/tutorials/basic/tutorial1/files/output_files/polyAT_vac_md1_12Acut.mdcrd.gz and http://ambermd.org/tutorials/basic/tutorial1/files/output_files/polyAT_vac_md1_nocut.mdcrd.gz are 48 bytes and 47 bytes, respectively. When decompressed, they show up as 0 bytes to the operating system.

We have previously used VMD successfully, and we are confused about what might be going wrong with the mdcrd files we generated. We would like to compare them to files that are known to work, but those files seem to be unavailable from the website/tutorial.

We’d appreciate any help you can offer with the VMD error or with access to the files missing from the tutorial. Thanks.

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Received on Mon Jul 02 2018 - 09:00:02 PDT
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