distance first time 10 :2014.NZ :429.OD1 out 2014NZ_429OD1.txt
Is above the syntax you used for distance measurement? why you are having
'first' there? That doesn't seem right.
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
>
>
--
Yi (Miranda) Shang
PhD candidate
Graduate Program in Molecular and Cellular Biology
Stony Brook University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Sep 19 2010 - 18:30:04 PDT
