AMBER Archive (2009)

Subject: [AMBER] rdparm bug?

From: Paul Mortenson (
Date: Tue Jul 07 2009 - 11:29:44 CDT


I think I may have found a bug in rdparm. I have tried to use it to
remove a single water from a box of waters, but the prmtop file
generated seems to get the two equilibrium bond lengths for TIP3P the
wrong way round (or equivalently, is labelling the bonds in the system
incorrectly). When I then use this prmtop file to calculate the energy
of the modified system, the calculated bond energy is enormous (~450000
kcal/mol). If I hack the prmtop file and swap the two equilibrium bond
lengths around, I get a much more sensible answer, which as expected is
close to the energy of the original system. I have attached a trivial
example illustrating this.

I'm using rdparm from a fully patched version of AmberTools 1.2, and
sander from AMBER 9. I'm running on CentOS Linux v4.6.

Thanks in advance for any help, and please let me know if I can provide
any more information.

Best regards,
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

  • application/x-compressed attachment: test.tgz

AMBER mailing list