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AMBER Archive (2007)Subject: AMBER: Sander....
From: Rita Cassia (Rita.Cassia_at_gmx.de)
Dear All,
I have followed a tutorial about MD simulation on DNA in Mixed Water-Ethanol Solvent (http://ludwig.chem.wesleyan.edu/~sergei/tutorial-2.htm).
The first two steps (min and init) had worked out. But the third, where I am supposed to run shake has not worked:
After typing: $AMBERHOME/exe/sander -O -i Etohshake.in -p ETOHBOX.top -c ETOHBOX_init.rst -oETOHBOX_shake.rst -x ETOHBOX_shake.crd
forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Inside the ETOHBOX_shake.rst there is the followed message:
-------------------------------------------------------
| Run on 04/03/2007 at 10:12:08
File Assignments:
Here is the input file:
md of ethanolbox
--------------------------------------------------------------------------------
| Flags:
I kindly ask if someone can help me to find out why there is a problem, if I'm doing exactly what the tutorial says.
If someone has some ideas or other input files to do minimization, equilibration of an ethanol box, (first NVT from 100K until 300K, then NPT at 300K, in order to equilibrate the density), it would help me a lot, since it is the first time I'm using sander.
Thanks in advance.
Rita Leite
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