[gmx-users] grompp warnings...

[Eva Stefanekova]

Hi, 
I am trying to run MD for protein-lipid complex. I included in topology file "protein.itp", "ffgmx.itp", "lipid.itp", "dmpc.itp". 
When I run preprocessing 
grompp -f em.mdp -c pro_lip.gro -p pro_lip.top -o pro_lip.tpr -maxwarn 1000 grompp gives some warnings like :

WARNING 1 [file "C:/gromacs/share/top/ffgmx.itp", line 6]:
  Found another defaults entry, will use the last one
WARNING 2 [file "C:/gromacs/share/top/ffgmxnb.itp", line 3]:
  Overriding atomtype O
WARNING 3 [file "C:/gromacs/share/top/ffgmxnb.itp", line 4]:
  Overriding atomtype OM
WARNING 4 [file "C:/gromacs/share/top/ffgmxnb.itp", line 5]:
  Overriding atomtype OA
WARNING 5 [file "C:/gromacs/share/top/ffgmxnb.itp", line 9]:
  Overriding atomtype OW
WARNING 6 [file "C:/gromacs/share/top/ffgmxnb.itp", line 11]:
  Overriding atomtype N
WARNING 7 [file "C:/gromacs/share/top/ffgmxnb.itp", line 12]:
  Overriding atomtype NT
WARNING 8 [file "C:/gromacs/share/top/ffgmxnb.itp", line 13]:
  Overriding atomtype NL
WARNING 9 [file "C:/gromacs/share/top/ffgmxnb.itp", line 14]:
  Overriding atomtype NR5
WARNING 10 [file "C:/gromacs/share/top/ffgmxnb.itp", line 15]:
  Overriding atomtype NR5*
WARNING 11 [file "C:/gromacs/share/top/ffgmxnb.itp", line 16]:
  Overriding atomtype NP
WARNING 12 [file "C:/gromacs/share/top/ffgmxnb.itp", line 17]:
  Overriding atomtype C
WARNING 13 [file "C:/gromacs/share/top/ffgmxnb.itp", line 18]:
  Overriding atomtype CH1
WARNING 14 [file "C:/gromacs/share/top/ffgmxnb.itp", line 19]:
  Overriding atomtype CH2
WARNING 15 [file "C:/gromacs/share/top/ffgmxnb.itp", line 20]:
.
.
.
WARNING 54.....
...
processing coordinates...
Warning: atom names in pro_lip.top and pro_lip.gro don't match (CN1 - CA)
Warning: atom names in pro_lip.top and pro_lip.gro don't match (CN2 - CB)
Warning: atom names in pro_lip.top and pro_lip.gro don't match (CN3 - CC)
Warning: atom names in pro_lip.top and pro_lip.gro don't match (NTM - N)
Warning: atom names in pro_lip.top and pro_lip.gro don't match (CA - CD)
Warning: atom names in pro_lip.top and pro_lip.gro don't match (CB - CE)
Warning: atom names in pro_lip.top and pro_lip.gro don't match (CC - CF)
Warning: atom names in pro_lip.top and pro_lip.gro don't match (CD - CG)
Warning: atom names in pro_lip.top and pro_lip.gro don't match (CE - CH)
WARNING 55 [file "pro_lip.top", line 20]:
  9 non-matching atom names
  atom names from pro_lip.top will be used
  atom names from pro_lip.gro will be ingnored

---------------------------------
Could anybody tell me, what these warnings means ?

Thanks in advance

Eva




 
















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