AMBER Archive (2009)

Subject: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE"

From: Jianping Lin (jianpingl_at_gmail.com)
Date: Mon Aug 10 2009 - 18:18:44 CDT

Dear All,

I still couldn't solve the "*RESTARTED DUE to LINMIN FAILURE" I had. when I
checked the structure using ptraj, It said that some distances between
Hydrogen and carbon are too small. I added the hydrogens using leap for my
structure.

The attactment includes my inital structure (without hydrogens) and inital
input for leap and sander.

Can someone show me how to solve this problem?
Thanks a lot.

Jianping
*
On 8/3/09, Jianping Lin <jianpingl_at_gmail.com> wrote:
>
> Dear All,
>
> I am learning how to use AMBER. When I minimize a protein structure in
> AMBER using "maxcyc=200, ncyc-1, imini=1, cut=12.0, igb=1, ntb=0, ntpr=1",
> I got the error "RESTARTED DUE to LINMIN FAILURE" and the output
> coordinate with all the number is NaN.
>
> Can someone tell me what it is going on with my simulation and how to solve
> it?
>
> Thanks a lot.
>
> Jianping
>



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