[gmx-users] Topology for hetroatom (PRODRG)

[Alok]

hello david,
                  I am attaching the rtp file for my LINKER (LIN)along 
with this mail.

                                    H                           O
                                     |                             ||
                       -CA-C(-N-CA-CB-N1)-C-CA-
                                ||                         |
                                O                       H1

The  linker section (-NH-CH2-CH2-NH-) attached to the carbonly group of 
two adjacent amino acids is as shown above.

Here CA and CB within my linker (shown in bold) atoms are of atom type CH2.

The rtp file for this linker was developed by checking the corresponding 
"atom types" from the database topology file of gromacs.

rtp file:
[ LIN ]
 [ atoms ]
    N      N    -0.28000      0
    H      H     0.28000      0
    CA   CH2     0.00000      1
    CB   CH2     0.00000      2
    N1     N    -0.28000      3
    H1     H     0.28000      3
 [ bonds ]
   N    H       gb_2
   N    CA      gb_20
   CA   CB      gb_26
   CB   N1      gb_20
   N1   H1      gb_2
   N1   +C      gb_9
[ angles ]
;  ai    aj    ak   gromos type
  -C    N       H       ga_31
  -C    N       CA      ga_30
   H    N       CA      ga_17
   N    CA      CB      ga_12
   CA   CB      N1      ga_12
   CB   N1      H1      ga_17
   CB   N1      +C      ga_30
   H1   N1      +C      ga_31
 [ impropers ]
;  ai    aj    ak    al   gromos type
   N    -C      CA      H       gi_1
   N1   CB      +C      H1      gi_1
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
   -CA   -C     N       CA      gd_4
   -C    N      CA      CB      gd_19
    N    CA     CB      N1      gd_17
    CA   CB     N1      H1      gd_19
    CA   CB     N1      +C      gd_19

But as i have mentioned before,pdb2gmx program does not read my LIN 
molecule.

Please suggest something.
                                              Thanking you,
                                                Alok Jain





David wrote:

>On Wed, 2005-02-23 at 22:26 +0530, Alok wrote:
>  
>
>>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..
>>    
>>
>
>rtp file.
>
>  
>
>>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. 
>>>
>>> 
>>>
>>>      
>>>
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>>
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