[gmx-users] Re: strangeness in gro file
Mark.Abraham at anu.edu.au
Thu Sep 15 03:35:59 CEST 2011
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.
> 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.
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