[gmx-users] .top file from .gro file

[Mark Abraham]

sunny mishra wrote:
> Hi Mark,
> I am sorry that I was not accurate in my scripts and I will not repeat this
> mistake again. Justin advised me that if the atoms are missing in  .itp file
> and .gro file (Some of them are actually missing) then I have to model the
> atoms back in the ORIGINAL PDB file but I din't quite get him. Can you help
> me out with this that how to model the original PDB file (1K4C) before I
> proceed.

That's not a trivial exercise, since you need to end up with a structure 
that looks "protein-like". There's probably software out there that will 
help (since it's a frequent issue), but I don't know anything about them.

Since it is a coarse-grained model, and you are only missing 7 sites, 
you might be best served by making educated guesses about approximately 
where the missing sites might be. They're probably missing from the 
original structure because they're sufficiently disordered that no data 
could be obtained about them, and so exactly where they are at the start 
of the simulation doesn't matter much - they'll move around lots. You'll 
need to understand what sites MARTINI creates (read their 
documentation!) in order to understand how you should "guess" where the 
missing sites might be. Then you edit in those atoms into your final 
.gro file, being sure to copy the columns of the formatting exactly, and 
update the number of atoms on the third (or so) line of the .gro file. 
You may have to be very careful massaging your EM and equilibration to 
not explode, if your guesses are not very good.

Mark