[gmx-users] ERROR when generated a rtp file with "grompp"

[Dallas Warren]

> I have 1*2097 + 780*38 + 7882*3 = 55383 atoms which suppose to be same
> in
> the .gro file.
> 
> If I modified my top to
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> DOD               779
> SOL              7882
> 
> it generate such errors :
> Warning: atom name 1 in topol.top and p_wateroil.gro does not match (C1
> - N)
> (more than 20 non-matching atom names)
> 
> WARNING 1 [file topol.top, line 19983]:
>   2053 non-matching atom names
>   atom names from topol.top will be used
>   atom names from p_wateroil.gro will be ignored
> 
> Anyone knows why and how to fix it?

The order of molecules in the top file has to match that in the gro file.  So, you have to check the gro file and list things in the correct order based on that.

Could be something like:

[ molecules ]
; Compound        #mols
DOD               779
Protein_chain_A     1
SOL              7882

Or even

[ molecules ]
; Compound        #mols
Protein_chain_A     1
DOD               700
SOL                82
DOD                79
SOL              7800

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.