AMBER Archive (2000)

Subject: Re: cion & LINMIN failure

From: takahas_at_bio.nagoya-u.ac.jp
Date: Mon Jun 26 2000 - 08:52:21 CDT

I solved my problem. Using parm96.dat was the source of LINMIN FAILURE. I
happened to find that the vdw radius of IM (CL- ion) is 0.0 in parm96.dat.
I was able to stop LINMIN FAILURE by using parm94.dat instead. Thanks for
giving me your replies, anyway.

Now, I am wondering why parm96.dat includes such a strange CL- ion.

------------------
Ken-ichi TAKAHASHI

At 00:38 00/06/25 +0900, I wrote:
>I encountered the LINMIN failure which seemed to be associated with
>counter ions.
>
>I added counter ions (2 to 14 ions) to an energy-minimized (100 to 150
>residues) protein by using cion. Then, I carried out energy minimization
>of the whole system. The run was terminated by the LINMIN failure. I tried
>tree proteins but I encountered the LINMIN failure in all cases. The
>following is the input file I used.
>
>min w/ harmonic restraints
> &cntrl
> imin=1, maxcyc=1000, ntpr=5,
> scee=1.2, idiel=1,
> cut=12.0, nsnb=20,
> ntr=1,
> &end
>Group input for restrained atoms
> 1.0
>RES 1 9999
>END
>END
>
>Is this the first report about the LINMIN failure caused by cion?
>How can I stop the LINMIN failure?
>
>Thank you for any help.