Hi Dhilip,
This is a well-known problem that has been discussed many times on the mailing list. The link provided at the bottom of your mdout file (i.e.,
http://amber.scripps.edu/Questions/linmin.html) has been replaced with
http://ambermd.org/Questions/linmin.html, where you can find more information.
In brief, this "error" means the minimiser hasn't satisfied its RMS convergence criterion, but can't find a good direction to try searching in.
If you're just minimising as a precursor to running molecular dynamics, it's not really a problem, because all you need worry about is that gross errors have been taken care of, which they will have been by this point.
If you are interested in getting a very low-energy structure (which is very difficult in an explicit water box anyway), you will probably want to look into the XMIN minimisation algorithms, as steepest-descents and conjugate gradients converge rather inefficiently.
Hope that helps,
Ben
On 18/5/2011, at 9:25 a.m., dhilip kumar ramalingam wrote:
> Dear Amer users,
> I am minimizing CI2 protein in water box . I am
> getting LINMIN failure. Can anybody solve the problem. Here is the .out
> file.
>
> <snip>
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
> ***** REPEATED LINMIN FAILURE *****
>
> ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO
> *****
>
> <snip>
>
> R.Dhilip kumar
> Computational Biophysics Lab
> Department of Biotechnology
> IIT Madras
> Chennai-600036
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed May 18 2011 - 08:30:02 PDT
