AMBER Archive (2002)

Subject: loss of disulfide bonds

From: Nicolas Le Novere (lenov_at_pasteur.fr)
Date: Mon Oct 14 2002 - 10:31:23 CDT

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) 

-- 
Nicolas LE NOVÈRE                                 
Récepteurs et Cognition,   Institut Pasteur,    75724 Paris cedex,        FRANCE
e-mail : lenov_at_pasteur.fr                       http://www-alt.pasteur.fr/~lenov
tel : 33-(0)1-45-68-88-44                              fax : 33-(0)1-45-68-88-36