spc2tip5p.m
- This function converts a .gro or .pdb file with spc water to some tip5p water
- The coordinate of the new MW center is set to OW coordinates, thus must be properly energy minimized this could easliy be avoided if using an unwrapped structure...
- The coordinate of the new MW centers is set to OW coordinates, thus must be properly energy minimized this could easliy be avoided if using an unwrapped structure...
Contents
Version
2.11
Contact
Please report problems/bugs to michael.holmboe@umu.se
Dependent functions
- import_atom.m
- write_atom_gro.m
- update_atom.m
Examples
- tip5p_atom = spc2tip5p('SOL.pdb')
- tip5p_atom = spc2tip5p('SOL.gro')
function tip5p_atom = spc2tip5p(filename) atom=import_atom_gro(filename); % Import the gro file nAtoms=size(atom,2); % Total number of atoms Ow_ind=find(strcmpi([atom.type],'Ow')); % find the index of the water-Oxygens SOL_ind=sort([Ow_ind Ow_ind+1 Ow_ind+2]); % find the index of the water-Hydrogens SOL_atom=atom(SOL_ind); % Extract the water into a new atom struct (why not just use atom.resname?) [SOL_atom.resname]=deal({'SOL'}); % Set the new resname nSOL=size(SOL_atom,2); % Number of water atoms new_SOL=[SOL_atom(1:3:end) SOL_atom(1:3:end) SOL_atom(1:3:end) SOL_atom(1:3:end) SOL_atom(1:3:end)]; % Create a new struct new_SOL(1:5:end)=SOL_atom(1:3:end); % assign Ow -> Ow new_SOL(2:5:end)=SOL_atom(2:3:end); % assign Hw -> Hw new_SOL(3:5:end)=SOL_atom(3:3:end); % assign Hw -> Hw new_SOL(4:5:end)=SOL_atom(1:3:end); % assign Ow -> Mw new_SOL(5:5:end)=SOL_atom(1:3:end); % assign Ow -> Mw [new_SOL(2:5:end).type]=deal({'HW1'}); % rename Ow -> Mw [new_SOL(3:5:end).type]=deal({'HW2'}); % rename Ow -> Mw [new_SOL(4:5:end).type]=deal({'LP1'}); % rename Ow -> Mw [new_SOL(5:5:end).fftype]=deal({'LP2'}); % rename Ow -> Mw % Put the new_atom struct back again into the original atom struct if SOL_ind(end) == nAtoms; tip5p_atom=[atom(1:SOL_ind(1)-1) new_SOL]; else tip5p_atom=[atom(1:SOL_ind(1)-1) new_SOL atom(SOL_ind(end)+1:nAtoms)]; end % Update the atoms index and stuff tip5p_atom=update_atom(tip5p_atom); % Write the new .gro file write_atom_gro(tip5p_atom,Box_dim,strcat('tip5p_',filename))