[AMBER] Sander crash, corrupt rst file...

From: Waqas Nasir <nasirwaqas1983.yahoo.com>
Date: Mon, 21 Dec 2009 03:44:42 -0800 (PST)

Hi all,
I have a protein-ligand system with 42000 atoms. I am running explicit solvent simulation. Every thing seems to be working fine except that the system has been crashed due to formatting error twice in the run. The error on the promopt looks like:

forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Image              PC        Routine            Line        Source            
sander             082120F7  Unknown               Unknown  Unknown
sander             08211717  Unknown               Unknown  Unknown
sander             081D70F6  Unknown               Unknown  Unknown
sander             081A0338  Unknown               Unknown  Unknown
sander             0819FFD3  Unknown               Unknown  Unknown
sander             081AD9A2  Unknown               Unknown  Unknown
sander             081AC3BF  Unknown               Unknown  Unknown
sander             080D3264  Unknown               Unknown  Unknown
sander             080D2F47  Unknown               Unknown  Unknown
sander             080A694C  Unknown               Unknown  Unknown
sander             08073067  Unknown               Unknown  Unknown
sander             08072B69  Unknown               Unknown  Unknown
sander             08048265  Unknown               Unknown  Unknown
sander             0821CE98  Unknown               Unknown  Unknown
sander             08048131  Unknown               Unknown  Unknown

When the system crashed, it corrupted the rst file, which means I can not run the simulation again from the rst file generated by sander. I then, generated rst file with ptraj but sander didnot read the time point and the temperature and everything. I understand that rst is just the coordinate information but then I feel a huge difference in the rst file I use from sander and the one I use from ptraj. Do you recommend that I continue with the ptraj rst file. or should I start my simulation again from the previous rst that I had for my md run?
Secondly, the rst file that was corrupted in the middle of the run read something like this in the beginning:

<null><null><null><null><null><null><null><null><null><null><null><null><null><null><null><null><null>.......
-8.1563957  35.5523092  37.4035340  -7.6259480  34.6225382  36.3334237
.
.
.
.
.
...
Does anyone has any idea of what might be going wrong? Or its just a bad luck...
Thanks,
Regards,
Waqas.

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Received on Mon Dec 21 2009 - 04:00:02 PST
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