AMBER Archive (2002)

Subject: Re: loss of disulfide bonds

From: Richard Henchman (rhenchma_at_mccammon.ucsd.edu)
Date: Mon Oct 14 2002 - 12:44:30 CDT

Would you please tell me what the syntax for the "crosslink"
command is? I can't seem to find it in the online manual or
updates. The error message almost helps:

crossLink: Improper number of arguments!
usage: crossLink <res1> <connect> <res2> <connect> [bondorder]

but I wanted to be sure. I had been using "bond" up until now.

Thanks,

Richard 

-- 
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
> 513 Parnassus Avenue                      
> University of California                  
> San Francisco, CA 94143-0446               
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>