AMBER Archive (2005)

Subject: AMBER: problem with position restraints (refc file)

From: pl (ladam_at_smbh.univ-paris13.fr)
Date: Tue Jan 18 2005 - 09:25:27 CST

Hi all,

I have a problem including position restraints during a sander SA run.
All works well if I don't use position restraints thought.

Here is what I do:
1) Run a simple min
2) run SA on the resulting min .rst file. I always end up with
the same error message that indicates that the refc file is not found
or not known:

  Unit 10 Error on OPEN: refc

and the REFC File assignment is not done as shown in the output file :

File Assignments:
| MDIN: anneal_smooth.in
| MDOUT: anneal_smooth.out
|INPCRD: PSN1_Quad_amb_anneal_cnst8_vdw_min_vac.rst
| PARM: PSN1_Quad_amb.top
|RESTRT: PSN1_Quad_amb_anneal_cnst8_vdw_anneal_smooth.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: PSN1_Quad_amb_anneal_cnst8_vdw_anneal_smooth.ene
| MDCRD: PSN1_Quad_amb_anneal_cnst8_vdw_anneal_smooth.trj
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

Here is how I invoke sander for this using a shell script:

#! /bin/csh -f
#--------------------------------------------------------------------------
echo " "
echo "SANDER: Minimization in Vacuo"
set RUN1 = min_vac
set PREFIX = PSN1_Quad_amb
echo $RUN1
echo $PREFIX
#--------------------------------------------------------------------------

sander -O \
       -i $RUN1.in \
       -o $RUN1.out \
       -p $PREFIX.top \
       -c $PREFIX.crd \
       -r $PREFIX'_'$RUN1'.rst' || goto error
       
echo "No errors detected"
echo "Converting" $PREFIX'_'$RUN1'.rst' "file as pdb: "
$PREFIX'_'$RUN1'.pdb'
ambpdb -p $PREFIX.top < $PREFIX'_'$RUN1'.rst' > $PREFIX'_'$RUN1'.pdb'
# /usr/local/VMD/vmd-1.8.2/bin/vmd -pdb $PREFIX'_'$RUN1'.pdb'

#--------------------------------------------------------------------------
echo " "
echo "SANDER Sim Ann with VDW and ELEC weight"
set RUN2 = anneal_cnst11_vdw
# set PREFIX = Quad_OK1_new_amb
echo $RUN2
echo $PREFIX
#--------------------------------------------------------------------------
# -ref $PREFIX'_min.rst' \
# -c $PREFIX.crd \

sander -O \
       -i $RUN2.in \
       -o $RUN2.out \
       -p $PREFIX.top \
       -c $PREFIX'_'$RUN1'.rst' \
     -ref $PREFIX'_'$RUN1'.rst' \
       -r $PREFIX'_'$RUN2'.rst' \
       -x $PREFIX'_'$RUN2'.trj' \
       -e $PREFIX'_'$RUN2'.ene' || goto error
       
echo "No errors detected"
echo "Converting" $PREFIX'_'$RUN2'.rst' "file as pdb: "
$PREFIX'_'$RUN2'.pdb'
ambpdb -p $PREFIX.top < $PREFIX'_'$RUN2'.rst' > $PREFIX'_'$RUN2'.pdb'
/usr/local/VMD/vmd-1.8.2/bin/vmd -pdb $PREFIX'_'$RUN2'.pdb'
exit(0)

error:
echo "--------------------------"
echo "Failure, check this out..."
echo "--------------------------"
exit(1)

And finally here is my SA script:

#-------------------------------------------------------------------------------
# Weight restraints
#-------------------------------------------------------------------------------
 &wt type='REST', istep1=0, istep2=3000, value1=1.0, value2=4.0,
&end
 &wt type='REST', istep1=3001, istep2=20000, value1=4.0, value2=4.0,
&end
                                                                               
 &wt type='END' &end
LISTOUT=POUT
DISANG= HBonds_Backb_CHI_PPA.rst

Group input for DNA restraints: 25 kcal/mol.
 25.0
RES 1 7
END
END
#---------------------------------------------------------------------------------

Simulated annealing protocol, 20 ps

&cntrl
    nstlim=20000,
    pencut=-0.001,
    ntpr=200,
    ntwx=200,
    ntt=1,
    cut=15.0,
    ntb=0,
    vlimit=10,
    ntr=1,
    nmropt=1,

&end
 
 &ewald
    eedmeth=5,
 &end
#
#------------------------------------------------------------------------
# Simulated Annealing Schedule
#------------------------------------------------------------------------ #
 &wt type='TEMP0', istep1=0, istep2=5000, value1=600., value2=600.,
&end
 &wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
value2=100.0, &end
 &wt type='TEMP0', istep1=18001, istep2=20000, value1=100.0,
value2=0.0, &end
                                                                               
 &wt type='TAUTP', istep1=0, istep2=5000, value1=0.4, value2=0.4,
&end
 &wt type='TAUTP', istep1=5001, istep2=18000, value1=0.4, value2=0.4,
&end
 &wt type='TAUTP', istep1=18001, istep2=19000, value1=0.4, value2=0.4,
&end
 &wt type='TAUTP', istep1=19001, istep2=20000, value1=0.4, value2=0.05,
&end

 &wt type='ELEC', istep1=0, istep2=5000, value1=0.0, value2=0.0,
&end
 &wt type='ELEC', istep1=5001, istep2=18000, value1=0.0, value2=0.0,
&end
 &wt type='ELEC', istep1=18001, istep2=19000, value1=0.0, value2=0.0,
&end
 &wt type='ELEC', istep1=19001, istep2=20000, value1=0.0, value2=1.0,
&end
#
#------------------------------------------------------------------------
# EOF
#------------------------------------------------------------------------ #
                                                                            
the ref file is here, it is readable, so I really don't know what's
happening at this point.
If someone can help...

Thanks again 

-- 
------------------------------------------------------------------
| Patrick LADAM                   |                               |
| Laboratoire CSSB                |     THE BIG BANG THEORY:      |
| UFR SMBH                        |                               |
| 74 rue Marcel Cachin            |   In the begining there was   |
| 93017 Bobigny CEDEX             |        nothing at all.        |
| >>> NEW e-mail: <<<             |                               |
| ladam_at_smbh.smbh.univ-paris13.fr |      Then, it exploded...     |
| Tel: 01 48 38 77 26 / 76 85     |                               |
| Fax: 01 48 38 77 77             |                               |
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