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Dr. Richard H. Henchman
Howard Hughes Medical Institute and Dept. of Chemistry & Biochemistry
Room 4202 Urey Hall, University of California, San Diego
9500 Gilman Drive, Dept. 0365, La Jolla, CA 92093-0365, USA
Tel: +1 (858) 822-1469, Fax: +1 (858) 534-7042
James W. Caldwell's message on Mon, Oct 14, 2002 at 10:28:15AM -0700 was:
>
> You need to add explicit bonds, either with "crosslink"
> or "bond". Crosslink is easier since you don't need
> to know the explicit atom number of your sulfur.
>
> jim
>
> On Mon, 14 Oct 2002, Nicolas Le Novere wrote:
>
> >Dear fellow AMBER users,
> >
> >I am sure my query is a common one among newbies, and in such a case I
> >apologize for the inconvenience. I am modelling a protein with several
> >disulfide bonds. The original PDB has been generated by MODELLER, so I
> >renammed CYS into CYX, and suppressed the inaccurate HG.
> >
> >Nevertheless, any manipulation with sander, like a minimization or an
> >equilibration cause my disulfide bonds to disappear, and therefore each
> >sulfur to move away.
> >
> >tleap session:
> >-------------
> >
> >wyman:~/NICMODEL/models/AMBER/a7ggSS$ tleap
> >-I: Adding /usr/local/amber6-ok/dat to search path.
> >-I: Adding /usr/local/amber6-ok/dat/leap/lib to search path.
> >-I: Adding /usr/local/amber6-ok/dat/leap/cmd to search path.
> >
> >Welcome to LEaP!
> >Sourcing leaprc: /usr/local/amber6-ok/dat/leap/cmd/leaprc
> >Log file: ./leap.log
> >Loading parameters: /usr/local/amber6-ok/dat/parm94.dat
> >Loading library: /usr/local/amber6-ok/dat/leap/lib/all_nucleic94.lib
> >Loading library: /usr/local/amber6-ok/dat/leap/lib/all_amino94.lib
> >Loading library: /usr/local/amber6-ok/dat/leap/lib/all_aminoct94.lib
> >Loading library: /usr/local/amber6-ok/dat/leap/lib/all_aminont94.lib
> >Loading library: /usr/local/amber6-ok/dat/leap/lib/ions94.lib
> >Loading library: /usr/local/amber6-ok/dat/leap/lib/water.lib
> >> loadAmberParams parm98.dat
> >Loading parameters: /usr/local/amber6-ok/dat/parm98.dat
> >> a7 = loadPDB a7 a7gg.pdb
> >loadPdb: Improper number of arguments!
> >usage: <variable> = loadPdb <filename>
> >> a7 = loadPDB a7gg.pdb
> >Loading PDB file: ./a7gg.pdb
> > total atoms in file: 16790
> >> solvateBox a7 WATBOX216 { 36 18 25 } 25
> > Solute vdw bounding box: 80.661 80.858 70.819
> > Total bounding box for atom centers: 152.661 116.858 120.819
> > Solvent unit box: 18.774 18.774 18.774
> > Total vdw box size: 80.661 80.858 70.819 angstroms.
> > Volume: 461889.977 A^3
> > Total mass 121428.180 amu, Density 0.437 g/cc
> > Added 0 residues.
> >> check a7
> >
> >[snips]
> >
> >Checking parameters for unit 'a7'.
> >Checking for bond parameters.
> >Checking for angle parameters.
> >check: Warnings: 264
> >Unit is OK.
> >> saveAmberParm a7 a7.prm a7.crd
> >
> >[snips]
> >
> > total 3635 improper torsions applied
> >Building H-Bond parameters.
> >Marking per-residue atom chain types.
> > (Residues lacking connect0/connect1 -
> > these don't have chain types marked:
> >
> > res total affected
> >
> > CTHR 5
> > NPHE 5
> > )
> > (no restraints)
> >
> >
> >Minimisation:
> >------------
> >sander -O -i min.inp -o min.out -p a7.prm -c a7.crd -x a7min.rst
> >min.inp:
> >
> >Minimization
> >first 10 cycles are by default SD then conjugent gradient
> > &cntrl
> > imin=1, ntx=1, ntf=1, maxcyc=100,
> > cut=15.0,
> > igb=1, gbsa=1,
> > ntb=0,
> > ntpr=10,
> > &end
> >
> >Equilibration:
> >-------------
> >
> >sander_classic -O -i eq.in -p a7.prm -c restrt -o a7eq.out -x a7eq.crd -r a7eq.rst
> >
> >eq.in:
> >
> > cold start belly equil
> > &cntrl
> > IREST = 0, ibelly= 1,
> > NTX = 1, TEMPI = 0.0,
> > NTB = 0, NRUN = 1,
> > NTT = 1, TEMP0 = 300.0, TAUTP = .1,
> > DTEMP = 2.0, NTP = 0,
> > NSTLIM= 1000, DT = .002,
> > NTC = 2,
> > NTF = 2,
> > IDIEL = 0, SCEE = 1.2,
> > CUT =999.0, NSNB = 9999,
> > NTPR = 20, NTWX = 20,
> > &end
> >Loop B
> >RES 147 154
> >RES 185 193
> >END
> >END
> >
> >(disulfide bonds are in the movable part)
> >
> >
>
> --
>
> ----------------------------------------------------------------------------
> James W. Caldwell (voice) 415-476-8603
> Department of Pharmaceutical Chemistry (fax) 415-502-1411
> Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
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> University of California
> San Francisco, CA 94143-0446
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>
Received on Mon Oct 14 2002 - 10:44:30 PDT