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).