AMBER Archive (2005)

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

From: pl (ladam_at_smbh.univ-paris13.fr)
Date: Wed Jan 19 2005 - 05:47:18 CST

Dear Carlos,
Please forgive me, I saw this morning I confused two sander scripts, so
I got it working now. I guess I was just too much tired yesterday. You
have to take a break sometimes...
Sorry again,
Sincerely

Le mardi 18 janvier 2005 à 12:36 -0500, Carlos Simmerling a écrit :
> 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_at_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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