Working directory: /home/zwei/work/MD/BPTI/charmm_pH/IM

Copy 6PTI.pdb to current directory

solvate.sh -ssbond -noblock(to compare with Amber simulation)

This will generate 6pti.pdb with standard terminus: NH3+  ----COO-, two ASP and two GLU are deprotonated with total of 882 atoms.

mkdir data

mkdir toppar

cp par_all22_prot_cmap_phmd.inp top_all22_prot_cmap_phmd.inp ./toppar

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

Copy add_h.inp to current directory.

Edit add_h.inp, make sure capping grous is "gene @segid first NTER last CTER setup".

charmm in=6pti <add_h.inp

This will generate 6pti_h.crd/pdb/psf in ./data/

Check 6pti_h.pdb, the total number of atoms will be 890, every ASP and GLU was protonated with two hydrogens.

 

Now we can run implicit solvent constant pH simulation with this input structure, if you plan to run in explicit solvent model, check the page of explicit solvent  model.

copy hphmd.inp to current directory, and edit the file as following.

........ set struct=data/@in_h ........ set time=2.0 !  ns set prfrq = 500 ........ mark off periodic boundary condition ......... mark off image atoms ......... gbsw sgamma 0.000 nang 50 conc 0.100 - sele .not. ( resn TIP3 .or. resn CLA .or. resn SOD ) end echeck -1 ! IMGfrq -1 ....... ! pconstant pmass 500.0 pref 1 pgamma 20 tbath 300.0 - ........ !ewald pmew fftx 64 ffty 64 fftz 64 kappa .34 spline order 6 stop

 

copy phmd-hybrid-g2.in & radius_gbsw.str to ./toppar/

 charmm <hphmd.inp