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On 15/09/2011 11:23 AM, Sweta Iyer wrote:
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cite="mid:E1E4AF78-D4C2-4AB8-9711-5E45CB3FFF0A@wehi.edu.au"
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<font class="Apple-style-span" color="#000000">Hi Mark,<br>
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I did a grompp without the temperature coupling and generated a
.tpr file. From that I generated a .gro file using editconf.
What it looks like now is it starts numbering from 1 -29, which
is where the first monomer ends, again 1-29 for the second
monomer and then its continuous numbering from then on! </div>
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That looks weird.<br>
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cite="mid:E1E4AF78-D4C2-4AB8-9711-5E45CB3FFF0A@wehi.edu.au"
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<div>DMPC starts from 30 and its continuous till the end of the
coordinate file! This still wouldnt let me generate an index
file as the numbering still overlaps between the two protein
chains. :(</div>
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As I said last time, the atom numbers in the coordinate file are not
significant. You can make them all zero, and make_ndx will still let
you make an index file that will work. Only the ordering is
significant. The contortions that I thought would regularize the
numbers were only to help you double check what is happening.<br>
<br>
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cite="mid:E1E4AF78-D4C2-4AB8-9711-5E45CB3FFF0A@wehi.edu.au"
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<div>Would it have a made a difference if, instead of including a
TER after one chain of the complex, I just changed the chain id
to distinguish them as separate entities in the original pdb
file that i used to begin with? I would have thought it shouldnt
make a difference and has nothing to do with this issue!</div>
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I don't know.<br>
<br>
Mark<br>
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