[gmx-users] Topology Manipulation question

[Marc Charendoff]

Hello,

I'm running grompp on two small molecules in a single
.gro file using the following topology file:

#include "ffgmx.itp"
#include "BDEX.ITP"
#include "AHL.ITP"
#include "spc.itp"

[ system ]
BDEX
AHL 

[ molecules ]
BDEX	   1
AHL     1

Part of my output looks like the following:

Back Off! I just backed up mdout.mdp to
./#mdout.mdp.2#
checking input for internal consistency...
calling cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter
combinations
Excluding 3 bonded neighbours for BDEX  1
Excluding 3 bonded neighbours for AHL     1
processing coordinates...
WARNING 1 [file "topol.top", line 12]:
  Bad box in file Complex.GRO
Generated a cubic box   20.000 x    1.445 x    1.830
Warning: atom names in topol.top and Complex.GRO don't
match (O2 - CAS)
Warning: atom names in topol.top and Complex.GRO don't
match (HAA - CAR)
Warning: atom names in topol.top and Complex.GRO don't
match (C2 - CAQ)
Warning: atom names in topol.top and Complex.GRO don't
match (C3 - CAP)
Warning: atom names in topol.top and Complex.GRO don't
match (O3 - CAO)
Warning: atom names in topol.top and Complex.GRO don't
match (HAB - CAN)
Warning: atom names in topol.top and Complex.GRO don't
match (C4 - CAM)
Warning: atom names in topol.top and Complex.GRO don't
match (O4 - CAL)
Warning: atom names in topol.top and Complex.GRO don't
match (C5 - CAK)
Warning: atom names in topol.top and Complex.GRO don't
match (C6 - CAJ)
Warning: atom names in topol.top and Complex.GRO don't
match (O6 - OAT)
Warning: atom names in topol.top and Complex.GRO don't
match (HAC - CAI)
Warning: atom names in topol.top and Complex.GRO don't
match (O5 - CAH)
Warning: atom names in topol.top and Complex.GRO don't
match (C1 - OAU)
Warning: atom names in topol.top and Complex.GRO don't
match (O1 - N)
Warning: atom names in topol.top and Complex.GRO don't
match (CAJ - HAA)
Warning: atom names in topol.top and Complex.GRO don't
match (CAK - CA)
Warning: atom names in topol.top and Complex.GRO don't
match (OBY - CB)
Warning: atom names in topol.top and Complex.GRO don't
match (CAL - CAA)
Warning: atom names in topol.top and Complex.GRO don't
match (OBZ - OAC)
(more than 20 non-matching atom names)
WARNING 2 [file "topol.top", line 12]:
  120 non-matching atom names
  atom names from topol.top will be used
  atom names from Complex.GRO will be ignored
 
- Complex.GRO consists of two molecules AHL and BDEX.
-The ffgmx force field has already worked successfully
with the BDEX.itp and molecule,  but for some reason
all but 2 of the AHL molecule atoms have the mismatch
problem. Which file do I have to modify to clear the
atom name mismatch issue? The atom names in question
are identical between the Complex.gro and AHL.itp
files, so I'm a bit confused. Any guidance you could
provide would be appreciated.

Regards,
Marc