AMBER Archive (2009)

Subject: RE: [AMBER] Sander imin=5 option

From: Paul Mortenson (P.Mortenson_at_astex-therapeutics.com)
Date: Tue Jun 16 2009 - 10:09:54 CDT

Apologies - I thought I was running with a fully patched version of
AMBER 9, but wasn't ($AMBERHOME was pointing to the wrong place). When I
repeated the experiment with the correct version, I get a clear message
in mdout saying that PBCs are not supported by imin=5. That doesn't
solve my problem, but is at least explicit - it seems I'll have to split
the trajectory up.

Thanks,
Paul

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
Behalf Of Carlos Simmerling
Sent: 16 June 2009 15:51
To: AMBER Mailing List
Subject: Re: [AMBER] Sander imin=5 option

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_at_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
>
>
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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.
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