are you up to date with all patches? if yes, forward your sander script and
mdin, as well as any errors in the mdout. also tell us what amber version
you are using.
On Tue, Jun 16, 2009 at 10:46 AM, Paul Mortenson <
P.Mortenson.astex-therapeutics.com> wrote:
> Dear All,
>
> I've been trying to use sander's imin=5 option for post-processing
> trajectories in AMBER 9, with little success. I managed to dig out this
> thread on the web:
>
> http://dev-archive.ambermd.org/200703/0017.html
>
> that seems to suggest that this option is broken, particularly where
> PBCs are being used. Has this ever been fixed? Is there another way I
> can achieve the same result, or will I have to split the trajectory into
> individual restart files and run sander separately on each?
>
> I'm running on CentOS Linux 4.6, just in case that affects anything.
>
> Thanks,
> Paul Mortenson
>
>
> Disclaimer
> 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
> P.Mortenson.astex-therapeutics.com 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 06 2009 - 09:46:46 PDT
