This is just a longer version of what I sent before.<br>It's not Shakespeare. I hope at least the worst spelling mistakes are gone.<br><br>----------------------<br><br>syntax (typical usage):<br><br> xpm2matrix hbond.ndx
groups1.ndx groups2.ndx [DA,AD] < hbmap.xpm > con.mat<br><br>Description:<br><br> This program reads .xpm files generated by "g_hbond -hbm ...",<br> and, for each frame in the trajectory, prints out a 2-dimensional table
<br> indicating which pairs of atoms (or residues, or groups of atoms)<br> are connected together (a connectivity matrix). This table may be easier<br> to interpret than the original .xpm file. As an input it requires a pair
<br> of files ("groups1.ndx" and "groups2.ndx" in this example) and each file<br> contains a list of groups. (Each group typically represents the atoms<br> belonging to each amino acid or nucleotide in a molecule.) Since there
<br> are two lists of groups, you can look at the connectivity matrix between<br> two different molecules. The the two lists of groups do not have to<br> correspond to residues from different molecules. They can be identical.
<br> The atoms in each group are not required to be donors or acceptors<br> (other atoms will be ignored). It is possible to tell xpm2matrix<br> to only consider the donor atoms from one group, and the acceptor atoms
<br> from another group. (See "DA" / "AD" below).<br> Again, groups do not have to correspond to residues. Of course, there<br> can be multiple donors and acceptors in each group, and more than one h-bond
<br> connecting each pair of groups. For example, one of list of groups<br> (say "groups2.ndx") might contain only a single group consisting of all<br> of the solvent atoms. In that case, for every frame in the trajectory
<br> xpm2matrix would simply report the number of water molecules bonded to <br> every residue/group in the molecule.<br><br>Output (stored in the "con.mat" file in the example above):<br><br> For each frame in the trajectory used to generate the xpm file, this
<br> program generates a connectivity matrix (delimited by spaces and newlines):<br><br>c11 c12 c13 ... c1n<br>c21 c22 c23 ... c2n<br>c31 c32 c33 ... c3n<br> : : : :<br>cm1 cm2 cm3 ... cmn<br><br> where cij = the number of hydrogen bonds connecting group i (from the
<br> first list of groups) with group j (from the second list)<br><br>Input:<br><br> hbmap.xpm An .xpm file created by "g_hbond -hbm" that you want to analyze<br> (See documentation for g_hbond.)
<br><br>Arguments:<br><br> hbond.ndx The ndx file created by "g_hbond -hbn ..."<br> groups1.ndx The number of hydrogen bonds is counted between every pair<br> groups2.ndx of groups in these two index files:
groups1.ndx & groups2.ndx.<br> DA or AD The 4th argument DA / AD is optional.<br><br> By using the "DA" and "AD" arguments, the user can limit<br> the atoms that the program considers from
groups1.ndx<br> and groups2.ndx. The DA command line argument causes<br> xpm2matrix to ignore all atoms from the first list of<br> groups which are not potential donor atoms, and all atoms
<br> from the second list which are not potential acceptors.<br> (The reverse is true for the AD command.)<br><br>Performance Issues:<br><br> This program can consume lots of memory, due to the order that data is
<br> saved to the xpm file, especially for long trajectories. If the program<br> is performing very slowly (running out of memory), you can get around the<br> problem by running g_hbond multiple times using the "-b" and "-e" flags,
<br> in order to generate multiple smaller .xpm files. You can run xpm2matrix<br> multiple times and concatenate the results together.<br><br><br>