Hi,
I have a problem with grompp.
I want to simulate membrane protein. I adjust the [ molecules ]
section to list the number and type of my components
I run grompp and it shows 56 warning about all of atom types in
ffG53a6nb.itp (56 atom types are in ffG53a6).
I run pdb2gmx for protein only. Why does it give me these warning?
I paste warning here:
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp
WARNING 1 [file ffG53a6nb.itp, line 3]:
Overriding atomtype O
WARNING 2 [file ffG53a6nb.itp, line 4]:
Overriding atomtype OM
WARNING 3 [file ffG53a6nb.itp, line 5]:
Overriding atomtype OA
WARNING 4 [file ffG53a6nb.itp, line 6]:
Overriding atomtype OE
WARNING 5 [file ffG53a6nb.itp, line 7]:
Overriding atomtype OW
WARNING 6 [file ffG53a6nb.itp, line 8]:
Overriding atomtype N
WARNING 7 [file ffG53a6nb.itp, line 9]:
Overriding atomtype NT
WARNING 8 [file ffG53a6nb.itp, line 10]:
Overriding atomtype NL
WARNING 9 [file ffG53a6nb.itp, line 11]:
Overriding atomtype NR
WARNING 10 [file ffG53a6nb.itp, line 12]:
Overriding atomtype NZ
WARNING 11 [file ffG53a6nb.itp, line 13]:
Overriding atomtype NE
WARNING 12 [file ffG53a6nb.itp, line 14]:
Overriding atomtype C
WARNING 13 [file ffG53a6nb.itp, line 15]:
Overriding atomtype CH0
WARNING 14 [file ffG53a6nb.itp, line 16]:
Overriding atomtype CH1
WARNING 15 [file ffG53a6nb.itp, line 17]:
Overriding atomtype CH2
WARNING 16 [file ffG53a6nb.itp, line 18]:
Overriding atomtype CH3
WARNING 17 [file ffG53a6nb.itp, line 19]:
Overriding atomtype CH4
WARNING 18 [file ffG53a6nb.itp, line 20]:
Overriding atomtype CH2r
WARNING 19 [file ffG53a6nb.itp, line 21]:
Overriding atomtype CR1
WARNING 20 [file ffG53a6nb.itp, line 22]:
Overriding atomtype HC
WARNING 21 [file ffG53a6nb.itp, line 23]:
Overriding atomtype H
WARNING 22 [file ffG53a6nb.itp, line 24]:
Overriding atomtype DUM
WARNING 23 [file ffG53a6nb.itp, line 25]:
Overriding atomtype S
WARNING 24 [file ffG53a6nb.itp, line 26]:
Overriding atomtype CU1+
WARNING 25 [file ffG53a6nb.itp, line 27]:
Overriding atomtype CU2+
WARNING 26 [file ffG53a6nb.itp, line 28]:
Overriding atomtype FE
WARNING 27 [file ffG53a6nb.itp, line 29]:
Overriding atomtype ZN2+
WARNING 28 [file ffG53a6nb.itp, line 30]:
Overriding atomtype MG2+
WARNING 29 [file ffG53a6nb.itp, line 31]:
Overriding atomtype CA2+
WARNING 30 [file ffG53a6nb.itp, line 32]:
Overriding atomtype P
WARNING 31 [file ffG53a6nb.itp, line 33]:
Overriding atomtype AR
WARNING 32 [file ffG53a6nb.itp, line 34]:
Overriding atomtype F
WARNING 33 [file ffG53a6nb.itp, line 35]:
Overriding atomtype CL
WARNING 34 [file ffG53a6nb.itp, line 36]:
Overriding atomtype BR
WARNING 35 [file ffG53a6nb.itp, line 37]:
Overriding atomtype CMet
WARNING 36 [file ffG53a6nb.itp, line 38]:
Overriding atomtype OMet
WARNING 37 [file ffG53a6nb.itp, line 39]:
Overriding atomtype NA+
WARNING 38 [file ffG53a6nb.itp, line 40]:
Overriding atomtype CL-
WARNING 39 [file ffG53a6nb.itp, line 41]:
Overriding atomtype CChl
WARNING 40 [file ffG53a6nb.itp, line 42]:
Overriding atomtype CLChl
WARNING 41 [file ffG53a6nb.itp, line 43]:
Overriding atomtype HChl
WARNING 42 [file ffG53a6nb.itp, line 44]:
Overriding atomtype SDmso
WARNING 43 [file ffG53a6nb.itp, line 45]:
Overriding atomtype CDmso
WARNING 44 [file ffG53a6nb.itp, line 46]:
Overriding atomtype ODmso
WARNING 45 [file ffG53a6nb.itp, line 47]:
Overriding atomtype CCl4
WARNING 46 [file ffG53a6nb.itp, line 48]:
Overriding atomtype CLCl4
WARNING 47 [file ffG53a6nb.itp, line 49]:
Overriding atomtype FTFE
WARNING 48 [file ffG53a6nb.itp, line 50]:
Overriding atomtype CTFE
WARNING 49 [file ffG53a6nb.itp, line 51]:
Overriding atomtype CHTFE
WARNING 50 [file ffG53a6nb.itp, line 52]:
Overriding atomtype OTFE
WARNING 51 [file ffG53a6nb.itp, line 53]:
Overriding atomtype CUrea
WARNING 52 [file ffG53a6nb.itp, line 54]:
Overriding atomtype OUrea
WARNING 53 [file ffG53a6nb.itp, line 55]:
Overriding atomtype NUrea
WARNING 54 [file ffG53a6nb.itp, line 56]:
Overriding atomtype SI
WARNING 55 [file ffG53a6nb.itp, line 57]:
Overriding atomtype MNH3
WARNING 56 [file ffG53a6nb.itp, line 58]:
Overriding atomtype MW
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6bon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Opening library
