AMBER Archive (2003)

Subject: Carnal processing of binary mdcrd files (IOUTFM=1) Sander 7

From: Chris Switzer (switzer_at_mail.ucr.edu)
Date: Wed Mar 19 2003 - 21:14:01 CST

Have run into the situation where carnal does not recognize a binary mdcrd input. Tried using the .gz and .Z extensions. Complaint is "Error filename.Z: format is neither pdb, crd or rst". The binary mdcrd was generated using Amber 7 sander, and IOUTFM=1. This is the first go at using binary format. Used the same procedure as for a formatted file in the sense that I just let the run go until it hits the file size limit at 2GB (and crashes; not very delicate). I tried carnal on the first 10,000 or so lines to give it some room to unpack, but still a no go. I would have assumed there needed to be a graceful termination of an md run so that formatting information gets written to the tail end of the file, except that when I tested this by doing 10 md-steps the binary output is still not read by Carnal. Also noticed that Carnal is possibly unchanged in the Amber 7 (per text output on screen indicating Amber 6.0, but I gather carnal 6 knows about binary). I can go back to formatte!
d outputs, but it would be nice if I could keep the 15 ns I have (+ like the compact format).

Any help much appreciated.

Chris Switzer

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Chris Switzer
Chemistry Department
UC Riverside
Riverside, CA
92521