[gmx-users] topology and rtp file

[irene farabella]

Hello Gmx Usrs,

I am new to Gromacs. I am trying to simulate a protein-membrane
complex using  berger-oplsaa combination . I have created a topology
file for the protein using pdb2gmx in order to then build up the
topology for my system using the include file mechanism.
After that I tried to use my system.top in grompp ( grompp -f xx.mdp
-c system.pdb -p system.top -o out.tpr ) but I get a warning about
atoms in top and pdb does not match. I went trough the mailing list
but I have still doubt. I checked where were the differences. It seems
that the order of the aromatic ring in the pdb and in the top didn't
match.

To be clear (tyr as example but the same problem occur with his):

.pdb  .top
 N         N
 HN        H
 CA       CA
 HA       HA
 CB       CB
 HB1     HB1
 HB2     HB2
 CG       CG
 CD1     CD1
 HD1     HD1
 CE1     CD2
 HE1     HD2
 CZ      CE1
 OH      HE1
 HH      CE2
 CD2     HE2
 HD2      CZ
 CE2      OH
 HE2      HH
 C            C
 O           O

Is this because the .top seems follow the order presents in the rtp
file that I have (am I right?).
Assuming that this is the case I am wondering if changing the atoms
order in the rtp from:

[ TYR ]
 [ atoms ]
    N    opls_238   -0.500     1
    H    opls_241    0.300     1
   CA    opls_224B   0.140     1
   HA    opls_140    0.060     1
   CB    opls_149   -0.005     2
  HB1    opls_140    0.060     2
  HB2    opls_140    0.060     2
   CG    opls_145   -0.115     3
  CD1    opls_145   -0.115     4
  HD1    opls_146    0.115     4
  CD2    opls_145   -0.115     5
  HD2    opls_146    0.115     5
  CE1    opls_145   -0.115     6
  HE1    opls_146    0.115     6
  CE2    opls_145   -0.115     7
  HE2    opls_146    0.115     7
   CZ    opls_166    0.150     8
   OH    opls_167   -0.585     8
   HH    opls_168    0.435     8
    C    opls_235    0.500     9
    O    opls_236   -0.500     9

to:

[ TYR ]
 [ atoms ]
   N    opls_238   -0.500     1
   H    opls_241    0.300     1
  CA    opls_224B   0.140     1
  HA    opls_140    0.060     1
  CB    opls_149   -0.005     2
 HB1    opls_140    0.060     2
 HB2    opls_140    0.060     2
  CG    opls_145   -0.115     3
 CD1    opls_145   -0.115     4
 HD1    opls_146    0.115     4
 CE1    opls_145   -0.115     6
 HE1    opls_146    0.115     6
  CZ    opls_166    0.150     8
  OH    opls_167   -0.585     8
  HH    opls_168    0.435     8
 CE2    opls_145   -0.115     7
 HE2    opls_146    0.115     7
 CD2    opls_145   -0.115     5
 HD2    opls_146    0.115     5
   C    opls_235    0.500     9
   O    opls_236   -0.500     9

can that have a further effect since it seems that the file handling
is based on line position and not atoms name.

Any suggestions are welcome

Thanks
Irene