On Fri, May 03, 2013, Poornima Iyer wrote:
> The system under my study is a dimer having 403 amino acids and two
> Mg+2 ions at the dimer interface. The .rst formed after second step of
> minimisation is comprised of the term "NaN".
> We also tried the keyword iwrap=1 in input file, but the result is same.
>
> Here is content of my input file.
>
> min2
> &cntrl
> imin=1,maxcyc=2500,ncyc=1000,
> cut=8.0,ntb=1, iwrap=1,
> ntpr=100,
> cut=8.0
> /
1. Use the checkoverlap command in ptraj to look for bad atom contacts in
the intial structure.
2. Set maxcyc=25 and ntpr=1; look carefully at the energies and the structure
you get.
...dac
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Received on Fri May 03 2013 - 12:00:02 PDT
