Hello all Amber users and Ross,
Out of necessity,I have to do a MD under explicit solvent by turning on the IGB flag. I have tested the case of the Amber Basic tutorial with explicit solvent
by setting IGB=1 and it's OK.In my system,a complex composed of DNA and proteins,I do MD by following the steps,first minimization,then heating stage,
then density stage,then equilibration stage,at last,the production stage.But if I turn on the IGB,the MD will crash with the calculating extending.
>From the error file produced,I got the following message:forrtl: severe (64): input conversion error, unit 9, file /home_soft/home/wujy/geyan/Amber/ABC_com_implicit/com_md5.rst
Then I searched the archive of Amber,and found Ross has discussed with others about this issue,
http://structbio.vanderbilt.edu/archives/amber-archive/2006/2736.php.Truely,my newly produced .rst file has **** in it.But now the question is by simply following her instructions,that is changing the ntx=6 won't work because it will bring the error like this: forrtl: severe (39): error during read, unit 9, file /home_soft/home/wujy/geyan/Amber/ABC_com_implicit/density.rst.Regarding the NTXO,as far as I know,the default value in Amber10 is 1.
So how to figure out this problem? I am very confused that if I don't turn on the IGB flag,and make other parameters the same as before,the whole process of MD will work well.
The details of my input is in attach.
Any suggestion is appreciated.
--------------
geyan
2010-05-06
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- application/octet-stream attachment: min.in
- application/octet-stream attachment: heat.in
- application/octet-stream attachment: equil.in
Received on Thu May 06 2010 - 01:30:04 PDT
