AMBER Archive (2002)

Subject: NMR restraints on a 10-mer DNA in Sander

From: Jo.Vinje_at_kj.uib.no
Date: Tue Nov 12 2002 - 11:34:55 CST

Dear fellow amber users,

I`am trying to run a nmr refinement in amber 6 of a oligonucleotide in explicit
water
using Example 3 in the amber 6 manual as a guide line. First I load my DNA in to
xleap and add counter ions and water so that I can create amber topology
and coordinate files. Then I want to carry out a minimization, optimizing just
the waters
and counterions, and keeping the solute fixed.

Here is the input file:

Initial min w/ position restraints on DNA
&cntrl
                                                                
    imin=1,
    ncyc=50, maxcyc=1000,
    nmropt=1,
    ntc=2, tol=0.000001,
    cut=9.0,
    ntpr=100,
    ntb=1,
    ntr=1,
 &end
 &wt type='REST', istep1=0,istep2=1000,value1=1.0,
             value2=1.0, &end
          
 &wt type='END' &end
LISTOUT=POUT
DISANG=RST
Group input for restrained atoms
  10.0
          
RES 1 20
          
END
          
END

This is just the same file as in example 3 in the amber 6 manual.

The sander commands:

snader -O -i min_wat_ion.in -o min_wat_ion.out -c gc.inpcrd -p gc.prmtop -r
min_wat_ion.restrt

Here is the output:

          -------------------------------------------------------
          Amber 6 SANDER Scripps/UCSF 1999
          -------------------------------------------------------

| Tue Nov 12 17:07:23 2002

  [-O]verwriting output

File Assignments:
|MDIN : min_wat_ion.in
|MDOUT: min_wat_ion.out
|INPCR: gc.inpcrd
|PARM : gc.prmtop
|RESTR: min_wat_ion.restrt
|REFC : refc
|MDVEL: mdvel
|MDEN : mden
|MDCRD: mdcrd
|MDINF: mdinfo

 Here is the input file:

Initial min w/ position restraints on DNA
&cntrl
                                                        
                                                                               
    imin=1,
    ncyc=50, maxcyc=1000,
    nmropt=1,
                                                                        
    ntc=2, tol=0.000001,
    cut=9.0,
                                                                         
    ntpr=100,
                                                                        
    ntb=1,
                                                                           
    ntr=1,
                                                                            
 &end
                                                                                
 
 &wt type='REST', istep1=0,istep2=1000,value1=1.0,
             value2=1.0, &end
                                                         
 &wt type='END' &end
                                                          
LISTOUT=POUT
                                                                  
DISANG=RST
                                                                      
Group input for restrained atoms
                                                      
  10.0
                                                                       
RES 1 20
                                                                      
END
                                                                          
END
                                                                                
  
                                                                               
-------------------------------------------------------------------------------

Initial min w/ position restraints on DNA

   1. RESOURCE USE:

 getting box info from bottom of parm
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found

   EWALD SPECIFIC INPUT:

 -------------------------------------------------
 NO EWALD INPUT FOUND: USING DEFAULTS
 -------------------------------------------------
     Largest sphere to fit in unit cell has radius = 23.572
     Calculating ew_coeff from dsum_tol,cutoff
     Box X = 50.172 Box Y = 47.144 Box Z = 61.626
     Alpha = 90.000 Beta = 90.000 Gamma = 90.000
     NFFT1 = 50 NFFT2 = 48 NFFT3 = 64
     Cutoff= 9.000 Tol =0.100E-04
     Ewald Coefficient = 0.30768
     Interpolation order = 4

 Warning: Error opening "Old" file from subroutine OPNMRG
 File = RST
                

>From this it seems like it is something wrong with the restraint file (RST),
but I have tested with different restraint files and still I get the same error
message. So I don`t think there is anything wrong with that file. Does any one
know what I`am doing wrong?

Thank you very much.
Jo