AMBER Archive (2002)

Subject: Re: loss of disulfide bonds

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Mon Oct 14 2002 - 11:49:15 CDT

you need to use the leap "crosslink" command.
see the manual.
Carlos

----- Original Message -----
From: "Nicolas Le Novere" <lenov_at_pasteur.fr>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Monday, October 14, 2002 11:31 AM
Subject: loss of disulfide bonds

> 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
>
>
>
>