[gmx-users] Re: strangeness in gro file

[Justin A. Lemkul]

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

========================================