You said that the "refc assignment is not done".
Do you mean that sander didn't do it? You need to tell sander
to do this since the default value is "refc". You need to put in your
script
"-ref XX" where XX is the name of the reference coordinates.
look at pages 92 and 101 in the manual.
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================
pl wrote:
>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
>
>
>
>
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Received on Tue Jan 18 2005 - 16:53:00 PST
