atom2make_ndx_bonded.m

This function can help you print one custom gromacs .ndx group,
based on the atomtypes names. You just have to pass on the two (or
three) atomtypes that makes up the bond, like {'Ohmg' 'H'}, or
{'Ohmg' 'Oh' 'H'}, which will find the bond between all
Ohmg/Oh - H. Note that you can use strncmpi to get a wider search.

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Examples

Version

2.11

Contact

Please report problems/bugs to michael.holmboe@umu.se

Examples

atom2make_ndx_bonded(filename,groupname,atomtypes) % Basic input arguments

function atom2make_ndx_bonded(filename,groupname,atomtypes)

atom = import_atom(filename);
atom = bond_angle_atom(atom,Box_dim,1.25,2.25);

if iscell(atomtypes)
    atomtypes=atomtypes;
else % if atomtypes
    ind=atomtypes;
end

if iscell(atomtypes)
    if numel(atomtypes)==2
        ind=[];
        str=sort(atomtypes);
        for i =1:size(Bond_index,1)
            temp_str=sort([atom(Bond_index(i,1:2)).type]);
            % Note that you can use strncmpi to get a wider search term
            if sum(strcmpi(temp_str,str))==2
                ind=[ind Bond_index(i,1:2)];
            end
        end
    elseif numel(atomtypes)==3
        ind=[];
        str1=sort(atomtypes([1 3]));
        str2=sort(atomtypes([2 3]));
        for i =1:size(Bond_index,1)
            temp_str=sort([atom(Bond_index(i,1:2)).type]);
            % Note that you can use strncmpi to get a wider search term
            if sum(strcmpi(temp_str,str1))==2
                ind=[ind Bond_index(i,1:2)];
            end
        end
        for i =1:size(Bond_index,1)
            temp_str=sort([atom(Bond_index(i,1:2)).type]);
            % Note that you can use strncmpi to get a wider search term
            if sum(strcmpi(temp_str,str2))==2
                ind=[ind Bond_index(i,1:2)];
            end
        end
    end
end


% Format the ind vector to have 15 entries per row
ext_ind=zeros(1,15*ceil(length(ind)/15));
ext_ind(1:length(ind))=ind;
ext_ind=reshape(ext_ind,15,[])';

% Print the index file
fid = fopen(strcat(groupname,'.ndx'), 'wt');
fprintf(fid, '%s %s %s\r\n','[',groupname,']');
for i = 1:size(ext_ind,1)
    row=ext_ind(i,:);
    row(row==0)=[];
    if max(row)<1000
        fprintf(fid, '%4i%4i%4i%4i%4i%4i%4i%4i%4i%4i%4i%4i%4i%4i%4i\r\n', row);
    elseif max(row)<10000
        fprintf(fid, '%5i%5i%5i%5i%5i%5i%5i%5i%5i%5i%5i%5i%5i%5i%5i\r\n', row);
    elseif max(row)<100000
        fprintf(fid, '%6i%6i%6i%6i%6i%6i%6i%6i%6i%6i%6i%6i%6i%6i%6i\r\n', row);
    end
end
fprintf(fid, '\r\n');
fclose(fid);

atom2make_ndx_bonded.m

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Examples