Mark Abraham wrote:
On 15/09/2011 11:23 AM, Sweta Iyer wrote:
Hi Mark,
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!
That looks weird.
I've seen this for dimeric proteins where the chains are identical. A little
annoying to deal with.
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. :(
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.
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!
I don't know.
genconf -renumber solves all of this rather easily, I think.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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