sorry, I see that below now, I had looked at the first sander run in the
script. It would mke it easier for me to follow if you could send the script
that actually generated the output with the error message. This script
and error output don't seem to go together, so it's harder to follow....
thanks
Carlos
pl wrote:
>Dear Carlos,
>
>That's what I did as said in my previous mail:
>
>.../...
>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'
>.../...
>
>But it stays to the default refc value, weird...
>
>Le mardi 18 janvier 2005 à 11:03 -0500, Carlos Simmerling a écrit :
>
>
>>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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>>
>
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Received on Tue Jan 18 2005 - 17:53:01 PST
