[AMBER] Error - PMEMD.MPI cannot understand line in rst file

From: <rohitarora10.gmail.com>
Date: Mon, 28 Oct 2013 12:34:22 +0100

Dear Amber users,

I am running MD simulations on a protein-ligand system using PMEMD.mpi
module of Amber.

I am running my production run in 4 stages (production01-04). When the stae
production03 ended, the rst file from this stage (production03.rst) was
supposed to be used to start production04. But when I start the
production04 stage, the simulation crashes and I see the following error in
the .out file:

ERROR: I could not understand line 17704
-62.9931150-161.5625896 250.5521926

So, I checked the production03.rst file at this line. Following is the

-372.9679572-128.0604962 -84.2870314-371.9935563-127.6363021 -83.2092619
-62.1664705-161.5757267 251.0346013 -61.5512698-162.0101636 250.4438183
-62.9931150-161.5625896 250.5521926
0.5038424 -0.0718586 0.0429195 -0.8019269 0.4793737 0.5508544

(The third line being the line #17704.)

I notice that this line is incomplete, but I can't understand why.

Has anyone come across a similar error? Is there any way to retrieve the
correct rst file without having to repeat the production03 stage?

I will appreciate any help in this matter.

Thank you

Best regards

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Received on Mon Oct 28 2013 - 05:00:02 PDT
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