[gmx-users] Halothane rtp and pdb file

[Poncho Arvayo Zatarain]

Hello, i want to run a simulation of halothane in a DPPC membrane. I have the pdb file of halothane and run the pdb2gmx (pdb2gmx -f halotano.pdb -o halotano.gro -water spc) with GROMOS 53a6 forcefield and the rtp file. The output marks this: Warning starting residue i825, 1493, -1442, -01715, -1239 in chain not identified as protein, DNA, RNA. Fatal error: Residue 1 not found in residue topology database. How can i solve this error? I think it could be a trouble with rtp or pdb file. I attached it. This is my rtp file 

bondedtypes ]
; bonds  angles  dihedrals  impropers
    7                        

[ HLT ]

 [ atoms ]
; name  type  charge  chargegroup       
   C1     C    0.66
   F1     F   -0.22
   F2     F   -0.22
   F3     F   -0.22
   C2     C    0.215
   Br     Br  -0.16
   Cl     Cl  -0.18
   H      H    0.125

 [ bonds ]
;atom1 atom2      b0      kb
     C2    H 
     C1    F1
     C1    F2
     C1    F3
     C2    Cl
     C2    Br
     C1    C2

 [ exclusions ]
;atom1 atom2

 [ angles ]
;atom1 atom2 atom3    th0    cth

 [ dihedrals ]
;atom1 atom2 atom3 atom4   phi0     cp   mult

 [ impropers ]
;atom1 atom2 atom3 atom4     q0     cq


And this is my halothane pdb file that i converted using OPEN BABEL 2.2




	
	
	
	


COMPND    3562 

AUTHOR    GENERATED BY OPEN BABEL 2.3.2
HETATM    1 BR  1   1.825  -1.412  -0.043  1.00 
0.00            

HETATM    2 CL  1   1.493   1.601  -0.049  1.00 
0.00            

HETATM    3  F  1  -1.442   0.983   0.438  1.00 
0.00             

HETATM    4  F  1  -0.715  -0.052  -1.340  1.00 
0.00             

HETATM    5  F  1  -1.239  -1.182   0.454  1.00 
0.00             

HETATM    6  C  1  -0.666  -0.040   0.010  1.00 
0.00             

HETATM    7  C  1   0.744   0.102   0.530  1.00 
0.00             

HETATM    8  H  1   0.765   0.103   1.623  1.00 
0.00             




END