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
>
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Received on Tue Sep 21 2010 - 08:00:05 PDT
