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 : http://www-alt.pasteur.fr/~lenov
tel : 33-(0)1-45-68-88-44 fax : 33-(0)1-45-68-88-36
Received on Mon Oct 14 2002 - 08:31:23 PDT
