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
Received on Tue Nov 12 2002 - 09:34:55 PST
