[gmx-users] Re: strangeness in gro file

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 15 03:56:37 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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