AMBER Archive (2005)

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

From: pl (ladam_at_smbh.univ-paris13.fr)
Date: Tue Jan 18 2005 - 11:13:17 CST

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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