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MolDyn |
# TEST#1:
# directory ./t1 shows example
to restore Hydrogen atoms whith geometry optimization and molDyn equilibration
The input PDB file does not have Hydrogen atoms
Job1:
1) add Hyrdogen atoms
2) make energy optimization
3) make molDynamics equilibration
command parameter file:
t1_MdynPar.inp :
#234567890123456789012345678901234567890!comment
#
$fullProtMD !all protein atom are moving i.e. are optimized
$SolvMod = GShell !USE Gaussian Solvation Shell Model
$engCalc ! do energy calculation
$engOptim ! do energy Optimization for moving atoms
$nOptStep=10 ! max N optim steps
$doMDyn ! do MolDynamics
$initMDTemp=10.00 ! initial Temperature in Kelwin
$bathMDTemp=100.0 ! thermal bath final Temperature
$runMDnstep=2000 ! do 2000 moldyn steps
$mdTimeStep=0.001 ! length of mdstep in ps
$nwtra=200 ! write snapshot PDB files each 200 md steps
#END
Run the test1:
> $MDYN09HOME/mDynQ09 -i t1_MdynPar.inp -c 1arb.0.pdb -mn 1arb -o t1.out
>
#NOTE! this command file t1_MdynPar.inp does not include $Hread keyword
therefore the program mdynQ09 will add XYZ of all Hydrogen atoms.
ALSO if some heavy atom of side chains are missing in the initial PDB file,
the program mdynQ09 will calculate coordinates of the side chain heavy atoms.
SEE test2.
#
TEST 1: console print out:
Status: 1 run mDynSB09 ...
Status: 2 run mDynSB09 ... Finish addHeavyAtom ...
Status: 3 run mDynSB09 ... file :molAddHvyAt.pdb
is written ...
Status: 4 run mDynSB09 ... Finish add_Hatoms ...
Status: 5 run mDynSB09 ... made molec topology ...
Status: 6 run mDynSB09 ... made [solvated] molec topology ..
Status: 7 run mDynSB09 ... init ForceField parameters ..
Status: 8 run mDynSB09 ... init Gauss Shell solvation model ..
Status: 9 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 10 run mDynSB09 ... initialXYZ energy calculation done ...
Status: 11 run mDynSB09 ... start energyOptimization ...
Status: 12 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 13 run mDynSB09 ... energyOpimization is done ...
Status: 16 run mDynSB09 ... start molDyn run ...
Status: 17 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 18 run mDynSB09 ... mdSnap : 2 is wrote ..
Status: 18 run mDynSB09 ... mdSnap : 2 is wrote ...
Status: 19 run mDynSB09 ... mdSnap : 3 is wrote ...
Status: 20 run mDynSB09 ... mdSnap : 4 is wrote ...
Status: 21 run mDynSB09 ... mdSnap : 5 is wrote ...
Status: 22 run mDynSB09 ... mdSnap : 5 is wrote ...
Status: 23 run mDynSB09 ... mdRunCall Finish: StepDone=ntimeS: 1004
Status: 24 run mDynSB09 ... eqvilibration mDyn is done ...
Status: 25 run mDynSB09 ... successful finish mDynSB program ...
#
*******************************************************
#
# TEST#2: initial PDB file has missing side chain atoms for some residues,
no all Hydrogen atoms
#
test2
restore missing side chain atoms for
VAL2, ASN7, ILE8, ARG18 which have missing side chain atoms in the initial pdb data file,
add Hydrogens,
do energy optimization and moldyn equilibration
In the Test #2
1) program AUTOMATICALLY adds all missing (in the initial pdb data file) side chain atoms
2) add all Hyrdogen atoms
3) makes energy optimization
4) makes molDynamics equilibration
#files to run test2:
#t2_MdynPar.inp
#234567890123456789012345678901234567890!comment
$fullProtMD !all protein atom are optimized
$SolvMod = GShell !USE Gaussian Solvation Shell Model
$engCalc ! do energy calculation
$engOptim ! do energy Optimization for all atoms
$nOptStep=3 ! max N optim steps
$doMDyn ! do MolDynamics
$initMDTemp=10.00 ! initial Temperature in Kelwin
$bathMDTemp=100.0 ! thermal bath final Temperature
$runMDnstep=2000 ! do 2000 moldyn steps
$mdTimeStep=0.001 ! length of mdstep in ps
$nwtra=200 ! write snapshot PDB files each 200 md steps
#END
~
run test2 by command
> $MDYN09HOME/mDynQ09 -i t2_MdynPar.inp -c 1arb.0.noHeavyAt.pdb -o t2.out
# program prints on console status of calculations:
tatus: 1 run mDynSB09 ...
Status: 2 run mDynSB09 ... Finish addHeavyAtom ...
Status: 3 run mDynSB09 ... file :molAddHvyAt.pdb
is written ...
Status: 4 run mDynSB09 ... Finish add_Hatoms ...
Status: 5 run mDynSB09 ... made molec topology ...
Status: 6 run mDynSB09 ... made [solvated] molec topology ..
Status: 7 run mDynSB09 ... init ForceField parameters ..
Status: 8 run mDynSB09 ... init Gauss Shell solvation model ..
Status: 9 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 10 run mDynSB09 ... initialXYZ energy calculation done ...
Status: 11 run mDynSB09 ... start energyOptimization ...
Status: 12 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 13 run mDynSB09 ... energyOpimization is done ...
Status: 16 run mDynSB09 ... start molDyn run ...
Status: 17 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 18 run mDynSB09 ... mdSnap : 2 is wrote ...
Status: 19 run mDynSB09 ... mdSnap : 3 is wrote ...
Status: 20 run mDynSB09 ... mdSnap : 4 is wrote ...
Status: 21 run mDynSB09 ... mdSnap : 5 is wrote ...
Status: 22 run mDynSB09 ... mdSnap : 6 is wrote ...
Status: 23 run mDynSB09 ... mdSnap : 7 is wrote ...
Status: 24 run mDynSB09 ... mdSnap : 8 is wrote ...
Status: 25 run mDynSB09 ... mdSnap : 9 is wrote ...
Status: 26 run mDynSB09 ... mdSnap : 10 is wrote ...
Status: 27 run mDynSB09 ... mdSnap : 10 is wrote ...
Status: 28 run mDynSB09 ... mdRunCall Finish: StepDone=ntimeS: 2004
Status: 29 run mDynSB09 ... eqvilibration mDyn is done ...
Status: 30 run mDynSB09 ... successful finish mDynSB program ...
#
******************************************************
TEST#3 in ./t3 directory
Job3:
1) read snapshot pdb file from TEST2
2) make energy optimization
3) restrain positions of ProteinBackBone atoms with harmonic force field
4) make md equilibration
5) make md simulated annealing by protocol in file t3_SAprotocol.inp
test3 is running by command
> $MDYN09HOME/mDynQ09 -i t3_MdynPar.inp -c 1arb.t3.inPdb.pdb -r1 t3_restrAt1.inp
-sa t3_SAprotocol.inp -mn 1arb -o t3.out
#files to run test3:
1) t3_MdynPar.inp:
#234567890123456789012345678901234567890!comment
$fullProtMD
$harmAt1PosRst=0.10 !harmConst=0.1 (kcal/A^2)
$Hread
$shake=2 !0/1/2! 2=all bonds are kept fixed
$SolvGS
$engCalc
$engOptim
$nOptStep=1 !max N optim steps
$doMDyn
$MDSA
$initMDTemp=10.00
$bathMDTemp=50.00
$runMDnstep=500
$mdTimeStep=0.002
$nwtra=250
#END
----------------
2) file t3_SAprotocol.inp :
#SA protocol
#each line start from keyword SAPROT
# ntimeMX tempTarget SCvdW wfHb128BB wfhB128BS
SAPROT 1000 100.0 1.0 1.0 1.0
SAPROT 1000 300.0 1.0 1.0 1.0
SAPROT 1000 100.0 1.0 1.0 1.0
SAPROT 1000 50.0 1.0 1.0 1.0
END
------------------------------------------------------------------------------------
3) file t3_restrAt1.inp :
#harmonically restrained RESidue segments
#(6x,2i4,a40)
RESTAT 1 263 PBB !PBB - ProtBackBone atoms are restrained, i.e. sideChain atoms are not
end restrained
!ALL - all atoms of residues are restrained
------------------------------------------------------------------------------------
consol run out
Status: 1 run mDynSB09 ...
Status: 2 run mDynSB09 ... made molec topology ...
Status: 3 run mDynSB09 ... made [solvated] molec topology ..
Status: 4 run mDynSB09 ... init ForceField parameters ..
Status: 5 run mDynSB09 ... init Gauss Shell solvation model ..
Status: 6 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 7 run mDynSB09 ... initialXYZ energy calculation done ...
Status: 8 run mDynSB09 ... start energyOptimization ...
Status: 9 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 10 run mDynSB09 ... energyOpimization is done ...
Status: 13 run mDynSB09 ... start molDyn run ...
Status: 14 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 15 run mDynSB09 ... mdSnap : 2 is wrote ...
Status: 16 run mDynSB09 ... mdSnap : 3 is wrote ...
Status: 17 run mDynSB09 ... mdSnap : 4 is wrote ...
Status: 18 run mDynSB09 ... mdSnap : 5 is wrote ...
Status: 19 run mDynSB09 ... mdSnap : 6 is wrote ...
Status: 20 run mDynSB09 ... mdSnap : 7 is wrote ...
Status: 21 run mDynSB09 ... mdSnap : 8 is wrote ...
Status: 22 run mDynSB09 ... mdSnap : 9 is wrote ...
Status: 23 run mDynSB09 ... mdSnap : 10 is wrote ...
Status: 24 run mDynSB09 ... mdSnap : 10 is wrote ...
Status: 25 run mDynSB09 ... mdRunCall Finish: StepDone=ntimeS: 2004
Status: 26 run mDynSB09 ... eqvilibration mDyn is done ...
Status: 27 run mDynSB09 ... mdSnap : 11 is wrote ...
Status: 28 run mDynSB09 ... mdSnap : 12 is wrote ...
Status: 29 run mDynSB09 ... mdSnap : 13 is wrote ...
etc.
Status: 30 run mDynSB09 ... successful finish mDynSB program ...
*****************************************************************************
TEST#4 in ./t4 directory
Job4:
1) read PDB file with H atoms
2) add positional restraints (harmonic force field) for defined atoms: file t4_restrAt1.inp
3) make energy optimization and molDyn
for list of residues shown in file t4_moveRes.inp
4) run simulated annealing via protocol in file: t4_SAprotocol.inp
run TEST4 by command
> $MDYN09HOME/mDynQ09 -c 1arb.t4.InPdb.pdb -i t4_MdynPar.inp -sa t4_SAprotocol.inp -mv t4_moveRes.inp
-r1 t4_restrAt1.inp -r2 t4_restrAt2.inp -rB t4_rigBody.inp -mn 1arb -o t4.out
#t4_MdynPar.inp
#234567890123456789012345678901234567890!comment
$MovingRes
$Hread
$hBond128 = 1.5
$compactForce = 0.25
$rigBody
$harmAt1PosRst=0.05 !harmConst (kcal/A^2)
$distRestrA2
$shake=1 !0/1/2
$SolvMod = GShell
$engCalc
$engOptim
$nOptStep=1
$doMDyn
$MDSA !do SimAnnealing
$initMDTemp=10.00
$bathMDTemp=50.00
$runMDnstep=500
$mdTimeStep=0.002
$NTV=1
$nwtra=250
#END
-------------
#t4_moveRes.inp : 1arb
aaaaaaIIIIiiii
#
MOVRES 91 179
MOVRES 190 240
end
------------
#t4_restrAt1.inp
#harmonically restrained RESidue segments
#xxxxxIIIIiiiiaaAAA
#(6x,2i4,a40)
RESTAT 1 63 ALL
RESTAT 64 179 PBB
RESTAT 200 250 PBB
end
-----------
# t4_restrAt2.inp
#harmonically restrained Atom-Atom distances
#1arb
#xxxxxx
#keyword atom1 atom2 distA HarmConst(kcal/mol*A^2)
RESTA2 ND2 ASN 222 : OG1 THR 219 = 7.0 1.5
RESTA2 O GLY 170 : OG1 THR 219 = 8.0 2.5
RESTA2 OH TYR 109 : OG1 THR 111 = 7.5 3.0
END
------------------------------------------------
#t4_rigBody.inp : 1arb
aaaaaaIIIIiiii
#
RIGB01 91 179
RIGB02 190 240
END
-------------------------------------------------
#t4_SAprotocol.inp
#SA protocol
#nSAstep
#4
#(f10.1,1x,f8.1,1x,3(f6.1,1x)
#234567890x12345678x123456x123456x123456
#ntimeMX tempTg SCvdW wfHb128BB wfhB128BS
SAPROT 1000 100.0 1.0 1.0 1.0
SAPROT 1000 300.0 1.0 1.0 1.0
SAPROT 1000 100.0 1.0 1.0 1.0
SAPROT 1000 50.0 1.0 1.0 1.0
END
-----------
test4 out to console:
Status: 1 run mDynSB09 ...
Status: 2 run mDynSB09 ... made molec topology ...
Status: 3 run mDynSB09 ... made [solvated] molec topology ..
Status: 4 run mDynSB09 ... init ForceField parameters ..
Status: 5 run mDynSB09 ... init Gauss Shell solvation model ..
Status: 6 run mDynSB09 ... mdSnap : 0 is wrote ...
Status: 7 run mDynSB09 ... initialXYZ energy calculation done ...
Status: 8 run mDynSB09 ... start energyOptimization ...
Status: 9 run mDynSB09 ... engOptimization step = 1 is done ...
Status: 10 run mDynSB09 ... mdSnap : 0 is wrote ...
Status: 11 run mDynSB09 ... energyOpimization is done ...
Status: 14 run mDynSB09 ... start molDyn run ...
Status: 15 run mDynSB09 ... mdSnap : 1 is wrote ...
Status: 16 run mDynSB09 ... mdSnap : 2 is wrote ...
Status: 17 run mDynSB09 ... mdSnap : 2 is wrote ...
Status: 18 run mDynSB09 ... mdRunCall Finish: StepDone=ntimeS: 504
Status: 19 run mDynSB09 ... eqvilibration mDyn is done ...
Status: 20 run mDynSB09 ... mdSnap : 3 is wrote ...
Status: 21 run mDynSB09 ... mdSnap : 4 is wrote ...
Status: 22 run mDynSB09 ... mdSnap : 5 is wrote ...
Status: 23 run mDynSB09 ... mdSnap : 6 is wrote ...
Status: 24 run mDynSB09 ... mdSnap : 6 is wrote ...
Status: 25 run mDynSB09 ... mdRunCall Finish: StepDone=ntimeS: 1004
Status: 26 run mDynSB09 ... mdSnap : 7 is wrote ...
Status: 27 run mDynSB09 ... mdSnap : 8 is wrote ...
Status: 28 run mDynSB09 ... mdSnap : 9 is wrote ...
Status: 29 run mDynSB09 ... mdSnap : 10 is wrote ...
Status: 30 run mDynSB09 ... mdSnap : 10 is wrote ...
Status: 31 run mDynSB09 ... mdRunCall Finish: StepDone=ntimeS: 1004
Status: 32 run mDynSB09 ... mdSnap : 11 is wrote ...
Status: 33 run mDynSB09 ... mdSnap : 12 is wrote ...
Status: 34 run mDynSB09 ... mdSnap : 13 is wrote ...
Status: 35 run mDynSB09 ... mdSnap : 14 is wrote ...
Status: 36 run mDynSB09 ... mdSnap : 14 is wrote ...
Status: 37 run mDynSB09 ... mdRunCall Finish: StepDone=ntimeS: 1004
Status: 38 run mDynSB09 ... mdSnap : 15 is wrote ...
Status: 39 run mDynSB09 ... mdSnap : 16 is wrote ...
Status: 40 run mDynSB09 ... mdSnap : 17 is wrote ...
Status: 41 run mDynSB09 ... mdSnap : 18 is wrote ...
Status: 42 run mDynSB09 ... mdSnap : 18 is wrote ...
Status: 43 run mDynSB09 ... mdRunCall Finish: StepDone=ntimeS: 1004
Status: 44 run mDynSB09 ... simulated annealing is done ...
Status: 45 run mDynSB09 ... successful finish mDynSB program ...
***********************