AMBER Archive (2000)

Subject: Re: cion & LINMIN failure

From: takahas_at_bio.nagoya-u.ac.jp
Date: Mon Jun 26 2000 - 04:24:01 CDT


Thank you for your reply. My edtin file is:

standard edtin
0 0 0 0
XYZ
OMIT
XRAY
0 0 0 0 0
QUIT

My prmin file is:

standard parm
BIN FOR MOD4
0 0 0
1

My counterions are NA+ and CL-. I added counterions using cion as follows:

(cion -elstat -p prmtop < min1.pdb > cion.pdb) >& cion.out

Thank you.
                                 Ken-ichi TAKAHASHI

At 09:50 00/06/26 -0700, you wrote:
>hi,
>can you show me your file_edit.in and your file_prm.in. What is your contrion?
>
>see you later.
>
>
>On Sun, 25 Jun 2000 00:38:24, takahas_at_bio.nagoya-u.ac.jp wrote:
> > Subject: cion & LINMIN failure
> > 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.
> >
> >
> > Ken-ichi TAKAHASHI
> >
> > ----------------------------------------------------------------
> > Division of Biological Science, Graduate School of Science, Nagoya
> University
> > Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
> > Phone: +81-52-789-2975 Fax: +81-52-789-2977
> >-- End of excerpt from takahas_at_bio.nagoya-u.ac.jp
>
>
>
>--
>***************************************************************************
>*****
>Pascal Bonnet pascal_at_qorws1.uab.es
>
>Unitat Quimica Organica and Institut de Chimie Organique et Analytique
>Facultat de Ciences UFR Sciences - UPRES-A 6005
>Universitat Autonoma de Barcelona Rue de Chartres - BP 6759
>08193 Bellaterra (SPAIN) 45067 ORLEANS CEDEX 2 -
>France
>Tel: 34935811266 Tel: 0238494577
>Fax: 34935811265
>***************************************************************************
>*****