mol2 file format in the future of amber

From: M. L. Dodson <bdodson_at_scms.utmb.EDU>
Date: Fri 20 Sep 2002 09:41:02 -0500 (CDT)

I have seen sporadic references to the use of the mol2 file format in
amber future development (in place of prep and frcmod files, IIRC).
Would anyone be able to furnish a paragraph or so of explanation of how
this would work? I do some special residue description development for
my work, and would like to make sure the scripts, etc. I write will not
need to be rewritten for the next version. For example, is there/will
there be a "prep2mol2" program available (other than the capabilities
built into antechamber or tleap)? Does this question even make sense?
:-)

Bud Dodson 


-- 
M. L. Dodson                                bdodson_at_scms.utmb.edu
409-772-2178                                FAX: 409-772-1790
From prbj_at_rediffmail.com 20 Sep 2002 16:42:14 -0000
Message-id: <20020920164214.1758.qmail.webmail8.rediffmail.com>
Date: 20 Sep 2002 16:42:14 -0000
From: Prem  Raj <prbj_at_rediffmail.com>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: (no subject)
In-Reply-to: <FB8942EA6DCDD511A43F00508BCF818D6F0B24.lajgrdexm01.agouron.com>
From prbj123_at_rediffmail.com 20 Sep 2002 17:27:07 -0000
Message-id: <20020920172707.21558.qmail.mailweb34.rediffmail.com>
Date: 20 Sep 2002 17:27:07 -0000
From: Prem  Raj <prbj123_at_rediffmail.com>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: vlimit and vmax
In-Reply-to: <FB8942EA6DCDD511A43F00508BCF818D6F0B24.lajgrdexm01.agouron.com>
Dear Amber users,
    I started a dynamics simulation on a protein molecule with  
explicit water using Amber 6 ( sander_classic). I am running it on 
an sgi iris platform. The initial minimisation ran without 
problem. when I started the equilibration md , I get the below 
error. How can I rectify this.
should I increase the value of vlimit ( the present value os 
15.0)
**********************
  vlimit exceeded for step            0; vmax =    
160.0023597269011
      COORDINATE RESETTING (SHAKE) WAS NOT ACCOMPLISHED
      WITHIN 3000 ITERATIONS
       A V E R A G E S   O V E R     2 S T E P S
  NSTEP =     2  TIME(PS) =    0.004  TEMP(K) =215744.72  PRESS 
=nan
  Etot   = nan           EKtot   = ************  EPtot      = 
nan
  BOND   =      78.1786  ANGLE   =     607.3218  DIHED      =     
967.8024
  1-4 NB =     818.2336  1-4 EEL =    6861.1856  VDWAALS    = 
nan
  EELEC  = nan           EHBOND  =       0.0000  CONSTRAINT =     
719.6468
  EAMBER (non-constraint) = nan
  EKCMT  = 1376096.1536  VIRIAL  = nan           VOLUME     =  
439846.6328
                                                 Density    =       
0.8016
  
------------------------------------------------------------------------------
===============================================================================
                       NMR restraints for step      3
  Energy (this step): Bond =    0.000   Angle =     0.000   
Torsion =     0.000
  Energy (tot. run) : Bond =    0.000   Angle =     0.000   
Torsion =     0.000
  DEVIATIONS:    Target=(r2+r3)/2                 Target = closer 
of r2/r3
             This step         Entire run        This step        
Entire run
            ave.    rms       ave.    rms       ave.    rms      
ave.     rms
  Bond      0.000   0.000     0.000   0.000     0.000   0.000     
0.000   0.000
  Angle     0.000   0.000     0.000   0.000     0.000   0.000     
0.000   0.000
  Torsion   0.000   0.000     0.000   0.000     0.000   0.000     
0.000   0.000
===============================================================================
       R M S  F L U C T U A T I O N S
  NSTEP =     2  TIME(PS) =    0.004  TEMP(K) =215597.13  PRESS 
=nan
  Etot   = nan           EKtot   = ************  EPtot      = 
nan
  BOND   =       6.4372  ANGLE   =      49.0044  DIHED      =       
2.9780
  1-4 NB =       0.3177  1-4 EEL =       4.0132  VDWAALS    = 
nan
  EELEC  = nan           EHBOND  =       0.0000  CONSTRAINT =     
719.6468
  EAMBER (non-constraint) = nan
  EKCMT  =  805150.9252  VIRIAL  = nan           VOLUME     =    
7049.3470
                                                 Density    =       
0.0128
  
------------------------------------------------------------------------------
  NMR restraints on final step:
  FATAL ERROR
> > 
> >************************************************************
> > >  Prem Raj B. Joseph
> > >  Dept. of Chemistry and Biochemistry
> > >  Howard Hughes Medical Institute
> > >  University of Maryland Baltimore County
> > >  1000 Hilltop Circle, Baltimore, MD 21250
> > >  Ph: (410)455-2718
> > >  email: prbj123_at_rediffmail.com
> > >
> > >Residence:
> > >  4747 Drayton Grn
> > >  Baltimore, MD - 21227
> > >  Ph(Res): (410)247-2413
> > 
> >*************************************************************
****************************
"Everyday is the first day of the rest of your life"
Dept. of Crystallography and Biophysics
University of Madras
Guindy Campus
Chennai 600 025
India
phone: 091 44 2300122, tele fax: 091 44 2300122
House Address:
25, Rangan Street
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Phone: 091 44 4353229
****************************
Received on Fri Sep 20 2002 - 07:41:02 PDT
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