[gmx-users] Re: strangeness in gro file

Mark Abraham 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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