[gmx-users] problem with Mn2+

[Yang Ye]

You would like to take a look at 

AMBER Parameter Database
http://pharmacy.man.ac.uk/amber/#org

How to migrate them into Gromacs? I am not familiar with Amber's Dummy atom
definition.

Yang Ye

MASS
MN     55.00     0.00        
KA     40.00     0.00        

NONB
  MN        1.6900     0.0140
  KA        1.7900     0.0140

  0  0  2

------calcium--------------
CAL
CAL  INT  0
CHANGE OMIT DU  BEG
 0.0
   1 DUMM  DU  M  0  -1  -2  0.000     0.000     0.000    0.000
   2 DUMM  DU  M  1   0  -1  1.0000    0.0000    0.0000   0.000
   3 DUMM  DU  M  2   1   0  1.0000   90.0000    0.0000   0.000
   4 KA    KA  M  29.683 127.561 -18.450  2.00
 
 
DONE
------manganese--------------
MNG
MNG  INT  0
CHANGE OMIT DU  BEG
 0.0
   1 DUMM  DU  M  0  -1  -2  0.000     0.000     0.000    0.000
   2 DUMM  DU  M  1   0  -1  1.0000    0.0000    0.0000   0.000
   3 DUMM  DU  M  2   1   0  1.0000   90.0000    0.0000   0.000
   4 MN    MN  M  29.683 127.561 -18.450  2.00
 
 
DONE
STOP

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Maximiliano Figueroa
Sent: Thursday, March 10, 2005 3:08 AM
To: David
Cc: Discussion list for GROMACS users
Subject: Re: [gmx-users] problem with Mn2+

I created Mn2+ in ffG43b1 and ffopls force fields. The parameters are
OK. With Hyperchem and Amber force field the problem is the same: the
Mn fly away from the active site. How I can simulated without lost the
Mn2+? (I have 2 Mn2+ in my active site)

Thanks


On Wed, 09 Mar 2005 19:35:12 +0100, David <spoel at xray.bmc.uu.se> wrote:
> On Wed, 2005-03-09 at 14:35 -0300, Maximiliano Figueroa wrote:
> > Dear Gromacs  users:
> >                                    We are working with a protein that
include
> > Mn2+ in the active site, using the parameter presented here some time
ago, we
> > were able to run some MD, but the Mn2+ fly away from the active site.
> > We try distance restraints but we received a error
> > Fatal error: [ file "mutanteSI.top", line 18748 ]:
> >              Atom index (1118) in distance_restraints out of bounds
(1-1)  ??
> >
> > Any hint to keep the Mn2+ in the active site will be relly very
appreciate!!
> Mn2+ has to be part of the protein to be able to use distance
> restraints. Are you sure force field is correct and ligation is not
> disturbed?
> >
> >                                                                Two crazy
boy
> > _______________________________________________
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>
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