BPTI constant pH

copy 6PTI.pdb to ./PH/

solvate.sh -ssbond(default: no crystal water, no ssbond,blocked)

the files generated include:

6pti_wb_ionized.pdb, 6pti_wb_ionized_charmm.psf,....

mkdir data

mv 6pti.pdb ./data/

mkdir toppar

cp par_all22_prot_cmap_phmd.inp top_all22_prot_cmap_phmd.inp ./toppar

Next, we add dummy hydrogen atoms to the carboxyl residues (Asp and Glu) using patches, ASPP2 and GLUP2.

cp add_h.inp to ./

charmm in=6pti <add_h.inp

the files generated include:

6pti_h.crd 6pti_h.pdb 6pti_h.psf

Let's solvate the protein and add ions to the water box.

copy water .crd to ./toppar

copy solvate.inp to ./

charmm in=6pti <solvate.inp

files generated include:

6pti_h_solvated.crd .pdb .psf .str  and 6pti_h_waterbox.crd .pdb .prm .str

now we add ions:

cp add_ions_hphmd.inp to ./

charmm in=6pti conc=0.100 <add_ions_hphmd.inp

files generated include:

6pti_h_ions.pdb .crd .str .prm

then we combine the structure

charmm in=6pti <minimize.inp

./data/6pti_h.solv.ion.min.psf  .pdb  .pbc  .crd

single pH simulation:

charmm <hphmd.inp

replica exchange pH simulation

mpirun -np 13 charmm <hphmd_phrex.inp

note: cp phmd-hybrid-g2.in phmd-hybrid-g2.in_0(  _1 _2.....)

for i in $(seq 1 13); do j=`expr $i-1|bc`; CptSX.pl 6pti.ph$i.lamb_$j 100 500000 $i; done

for i in $(ls *.sx); do string+=" $i"; done

cptpKa.pl bpti $string

gnuplot combine_gnuplot

 

 

residue pka reference
ASP_3 2.45 3.71
GLU_7 2.93 4.15
LYS_15 9.40 10.67
LYS_26 9.39 10.67
LYS_41 10.02 10.67
LYS_46 9.48 10.67
GLU_49 2.86 4.15
ASP_50 2.26 3.71

 

discard the following

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Table I is calculated pKa of residue 3ASP,7GLU,15LYS,26LYS,41LYS,46LYS,49GLU,50ASP,(symmetric?) the simulation time is 0.01ps(2.63h on sun).

pK1/2 of titrable residues in BPTI" width="500" colwidth="20|100|50" colalign="left|left|center|left|right
#res name trial1 trail2 trial3 trial4 trial5 ave\pmstd
3 ASP 0.46 2.80 1.04 1.73 2.41 1.69\pm0.96
7 GLU 5.05 5.66 5.75 5.61 5.95 5.60\pm0.34
15 LYS 9.86 10.72 11.57 10.40 10.30 10.57\pm0.64
26 LYS 10.27 11.13 13.41 9.20 10.04 10.81\pm1.61
41 LYS 9.50 8.59 13.38 12.86 12.98 11.46\pm2.24
46 LYS 12.99 13.03 13.41 12.86 12.98 13.05\pm0.21
49 GLU 2.75 3.17 5.01 3.98 3.78 3.74\pm0.86
50 ASP 0.52 1.52 4.49 2.23 0.86 1.92\pm1.58

BPTI_titration