Dear Sir
As per your suggestion I looked into the equil1.rst file and I do see the *'s at 1449 line as you have pointed out in the reply mail.
Would like to know how to overcome this problem. My initial structure is a homology modelled protein (without any restrain being specified) . Any tutorial, if you can suggest will be of great help to me
Yours sincerly
Ramesh K V
________________________________
From: Ross Walker <ross.rosswalker.co.uk>
To: 'kureeckal ramesh' <kureeckalramesh.yahoo.co.in>; 'AMBER Mailing List' <amber.ambermd.org>
Sent: Thursday, 1 December 2011 9:39 AM
Subject: Re: [AMBER] error in MD simulation
Hi Ramesh,
See line 1449 of the equil1.rst file:
62.1879466 -69.3482739 25.9323445 61.1375251 -67.5513729 26.5848404
************************2790.5122819************ 267.5241538************
************************************************************ 74.7837402
************************************7413.3591272************************
0.0762921 -0.1645321 -0.0339564 -0.2831368 -0.2623048 -0.2482094
The *'s mean the values are too large for the space allocated. Looks like
your system blew up during the heating phase. I suggest looking carefully at
the output from the heating. Visualize the mdcrd file. It looks like
whatever is at the end of your molecule is flying off into space. This
should show up as large bond energies etc in the mdout file. Often such
things are caused by having atoms sitting on top of each other in your
initial input coordinates or having very a very strained initial structure.
All the best
Ross
> -----Original Message-----
> From: kureeckal ramesh [mailto:kureeckalramesh.yahoo.co.in]
> Sent: Wednesday, November 30, 2011 7:42 PM
> To: amber.ambermd.org
> Cc: sudhadeshmukh.yahoo.com
> Subject: [AMBER] error in MD simulation
>
> Dear AMBER user
>
> I am running my protein sample for MD simulation (solvent effect) for
> 10 ns (on SGI altix UV 10) . Was able to complete sucessfully heating
> stage. While running the producition stage, the program was able to
> complete only the first stage (500 ps) and thereafter it was not able
> to progress. The error showed is as follows:
> -----------------------------------------------------------------------
> -----------------------------------------------------------------------
> --------------------------ramesh.sgiUV:~> ./PROD.sh
> forrtl: severe (64): input conversion error, unit 9, file
> /home/ramesh/equil1.rst
> Image PC Routine Line Sou
> rce
> sander 0000000000C0BF9D Unknown Unknown Unk
> nown
> sander 0000000000C0AAA5 Unknown Unknown Unk
> nown
> sander 0000000000BA3D49 Unknown Unknown Unk
> nown
> sander 0000000000B3D30A Unknown Unknown Unk
> nown
> sander 0000000000B3CB00 Unknown Unknown Unk
> nown
> sander 0000000000B676DB Unknown Unknown Unk
> nown
> sander 00000000004E9835 Unknown Unknown Unk
> nown
> sander 00000000004ABDED Unknown Unknown Unk
> nown
> sander 00000000004AA85C Unknown Unknown Unk
> nown
> sander 00000000004051CC Unknown Unknown Unk
> nown
> libc.so.6 00002B249A274BC6 Unknown Unknown Unk
> nown
> sander 00000000004050C9 Unknown Unknown Unk
> nown
> gzip: equil2.mdcrd: No such file or directory
>
> Unit 30 Error on OPEN:
> equil2.rst
>
>
>
> gzip: equil3.mdcrd: No such file or directory
>
> Unit 30 Error on OPEN: equil3.rst
>
> ........
> ........
>
> Unit 30 Error on OPEN:
> equil19.rst
>
>
>
> gzip: equil20.mdcrd: No such file or directory
> DONE
> -----------------------------------------------------------------------
> -------------------------------------------------------
> To me it appears some thing wrong in equil1.rst file, which I am not
> able to figure it out. I am attaching the equil1.rst file I used for
> simulation
>
>
> request you to kindly suggest solution to my problem
>
> Thanking you
> Ramesh K V
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Received on Wed Nov 30 2011 - 21:30:04 PST
