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-- Yong Duan, Ph.D, Professor UC Davis Genome Center and Department of Biomedical Engineering University of California at Davis Davis, CA 95616 530-754-7632 On 11/30/11 9:24 PM, "kureeckal ramesh" <kureeckalramesh.yahoo.co.in> wrote: >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 > > >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber >_______________________________________________ >AMBER mailing list >AMBER.ambermd.org >http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Nov 30 2011 - 23:00:03 PST