[gmx-users] Topology for hetroatom (PRODRG)

[Alok]

Hello David,
                        I include my linker molecule (defined as LIN )in 
the rtf and hdb files. i also add this LIN in aminoacids.dat file 
because i want to consider this linker as a part of protein. I also 
increase the  total count in aminoacids.dat file by one.
    but pdb2gmx  program does not reconize my linker lolecule (LIN)
i encounter follwing fatal error..

Fatal error: Residue 'LIN' not found in residue topology database

i also check the pdb2gmx.log file (flag -debug) in which it is not 
reading my linker molecule.

part of the ouput from the log file generated by pdb2gmx which shows the 
molecules read by the program from the rtf file is as :

 80    AR     1          0          0          0          0          0
 81 SO42-     5          4          6          0          0          0
 82  ZN2+     1          0          0          0          0          0
 83   NA+     1          0          0          0          0          0
 84   CL-     1          0          0          0          0          0
 85  CA2+     1          0          0          0          0          0
 86  MG2+     1          0          0          0          0          0
 87  CU1+     1          0          0          0          0          0
 88  CU2+     1          0          0          0          0          0
 89   H2O     3          3          0          0          0          0
 90   HOH     3          3          0          0          0          0
 91   HO4     4          3          0          0          0          0
 92  H2OE     3          3          0          0          0          0
 93 CHCL3     5          9          0          0          0          0
 94  DMSO     4          6          0          0          0          0
 95 CH3OH     3          3          0          0          0          0
 96  CCL4     5          9          0          0          0          0
 
Here in this output i do not find my LIN molecule which is defined after 
CCL4 in the rtf file.

Am i going wrong somewhere?? Please suggest.
                                                                        
      Thanking you,
                                                                        
          Alok Jain


David wrote:

>On Wed, 2005-02-23 at 11:52 +0530, Alok wrote:
>  
>
>>hello David,
>>                   Thank you for your reply.So we will include our 
>>linker section molecule in the rtf and hdb files.But we are still not 
>>sure of the parameters we are to take for the linker molecule.Should I 
>>directly take the parameters mentioned in the ' itp file ' generated by 
>>the PRODRG server ??????
>>                          The linker section forms a covalent bond with 
>>the peptide.The carbonyl group at both ends of the peptide 
>>(XXX-NH-CH2-CH2-NH-XXX) forms a covalent bond with the amino group at 
>>the ends of the linker section.
>>                                           
>>    
>>
>It depends on your force field. 
>
>  
>