Re: [AMBER] error in MD simulation

From: Yong Duan <duan.ucdavis.edu>
Date: Wed, 30 Nov 2011 22:31:14 -0800

You may want to have a thorough energy minimization to remove the strain
before start the simulation. This is always a good practice even for
well-refined high resolution structures.

--
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/amber
Received on Wed Nov 30 2011 - 23:00:03 PST
Custom Search