AMBER Archive (2002)

Subject: Re: loss of disulfide bonds

From: Natasja Brooijmans (nbrooij_at_itsa.ucsf.edu)
Date: Mon Oct 14 2002 - 11:46:54 CDT

If you7 leave in the PDB CONECT records for the disulfides they should be
bonded automatically by leap, but please make sure to check this visually.

Natasja

Natasja Brooijmans
Graduate Program in Chemistry & Chemical Biology
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco, CA 94143-0446
phone: 415-476 8291
fax: 415-502 1411
e-mail: nbrooij_at_itsa.ucsf.edu

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)
>
> --
> 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
>
>
>
>