Kushal Seth wrote:
Dear All!
Thanks for your replies.My CPP path seems to be ok as far as the location is concerened and I continue to get the same error messsages.

The fact that you are receiving a cpp exit code (32512 in your email) means it is being found and run, so Sukit's suggestion isn't applicable here.

Is there any other reason for that ( my top files also seem to be wroking for other simulations )

Reading the error message carefully will usually help you...

     >     -------------------------------------------------------
     >     Program grompp, VERSION 3.3
     >     Source code file: grompp.c, line: 427
     >
     >     Fatal error:
     >     number of coordinates in coordinate file
     >     (binaryCR-Ochol-box-largeZ.pdb, 10280)
     >                 does not match topology (mytop-nowater1.top, 0)

The absence of atoms in your .top file suggests that it is not being generated correctly, or is trying to include non-existent files. Have a look at it and try work out what is going wrong.

Mark
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