AMBER Archive (2009)

Subject: [AMBER] Max filename length in Sander?

From: Paul Mortenson (
Date: Mon Jun 08 2009 - 05:59:52 CDT

Dear AMBER users,

I think I may have found a small bug / feature in AMBER9. Specifically,
it seems that when periodic boundary conditions are turned on, the
maximum filename length for the inpcrd file is 80 characters. From
looking at the code, it would seem that the limit for this value should
be a much more reasonable 256 characters. Interestingly, with PBCs
turned off, this limit doesn't seem to apply. I have attached a
small(ish) test job that hopefully will allow this to be reproduced,
along with the output that I see.

I am not sure whether the same is true for other input filenames. I have
seen the same problem with PMEMD9. I have a fully patched (as of this
morning) version of AMBER9, running on CentOS 4.6.

Thanks in advance for your help,

Paul Mortenson

This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing and destroy all copies of the message and any attached documents.
Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674

AMBER mailing list