MolDyn

Test examples description


# 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 ...

***********************