Hi Dan
Will do. I ran a very short run over night with my large system. It (the
trajectories size) should be small enough not to be a problem to email.
However, I don't have access at the moment to the data but will get them
to you by this evening for sure!!
Thanks for looking into this. My computer/AMBER software savvy is very
limited and so, I am in over my head....but I am learning.
Cheers, Steve
Steve Seibold, Ph.D.
Assistant Professor of Chemistry
University of Saint Mary
4100 S. 4th Street
Leavenworth, KS 66048
seibold79.stmary.edu
Tel: 913 758 6294
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Tuesday, September 21, 2010 9:31 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Blowing array
Hi,
I can't reproduce your ptraj error using similar input; however, I am
running it on a smaller system (only ~40K atoms) so it could be that
system size is an issue. Could you possibly send along the topology
file you are using along with 1 frame of the coordinates so I can
attempt to reproduce the error here? Thanks.
-Dan
On Sun, Sep 19, 2010 at 7:00 PM, Seibold, Stephen <Seibold79.stmary.edu>
wrote:
>
>
> Hi AMBER
> Thanks everyone for their response. May be I should give some history
to my reoccurring problem...it may help??
>
> I purchased AMBER11 with the newest version of AmberTools. I have
compiled it at mutiple times and each time it gets stuck on the AMBER
test jobs running specific inputs for PIMD. I commented those out and
then it compiled fine.
> However, with this version of AMBER, I could not get distance
measurements for my protein (got errors of blown arrays) and finally
thought I would start from scratch. So, I recompiled AMBER and Tools and
began doing tutorials from the amber web site. I did get it to work
(i.e. distance measurements) for the DNA tutorial one and was thinking
it was alright now. However, when I took trajectories generated with
AMBER11 for my protein I once again got errors. I am now I am getting
"segmentation faults". I am not sure why the error has changed from
"blowing arrays". I am sending you the input file for getting those
trajectories also.
>
> I am using the newest version of ptraj and have applied all the
bugfixes. I am sending you the input and output log file on the Distance
measurement failure. I would send you my trajectories but they are very
large. The problem seems to be (so far) only the distance measurements.
For example, calculating RMSD does not appear to be a problem.
>
> Thanks so much again for your help.
>
> Please let me know if there is something more I can tell you, send you
to help me resolve this issue.
>
> Steve
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Sep 21 2010 - 08:00:09 PDT
