At 02:05 PM 4/12/2004, you wrote:
>Hi, I am using SANDER to minimize the energy of DNA before I calculate its
>frequencies using NMODE. Because I do not want to restrain any atoms in
>the mimization, so there is no group information in my input file for
>sander. However, I got an error message " sandermin.in, Group is not found
>at the end of file". Is the group information required for any
>minimization in sander? Thank you!
Make sure you do not have nmropt=1 or other group requiring option.
In case it might help, here is a valid minimization input file for sander
that does not have a group. (It was generated by MM_PBSA - so the options
are of course very different from what you will want to use).
File generated by mm_pbsa.pl. Using MM GB MS
&cntrl
ntf = 1, ntb = 0, dielc = 1,
idecomp= 0,
igb = 1, saltcon= 0.2,
offset = 0.09, extdiel= 78.5,
gbsa = 1, surften= 1.0,
cut = 99999.0, nsnb = 99999,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 1, ncyc = 0,
&end
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Received on Mon Apr 12 2004 - 20:53:01 PDT
