[gmx-users] Topology for hetroatom (PRODRG)

[Alok]

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.
                                                                        
                                                                        
                 Thank you,
                                                                        
                                                                        
                    Alok Jain
                                       
David wrote:

>On Tue, 2005-02-22 at 19:17 +0530, Alok wrote:
>  
>
>>hello gmx users,
>>               i want to simulate a peptide-linker-peptide system. The
>>system is XXX-NH-CH2-CH2-NH-XXX where X represents the
>>standard amino acids.
>> To simulate this system i want to first generate a topology file for the
>>linker section of the system.I did so by using  PRODRG server by suppling
>>the linker section as the input..
>>    
>>
>
>you want to do this manually in the rtp file and hdb files. chapter 5 in
>the manual. you didn't say where the NH groups should bind to. in
>addition check out the specbond.dat file.
>
>
>  
>
>>                  The input coordinate file to the server and the output
>>from the server are as follows:
>>
>>Input:
>>HETATM   14  N     2     2      -0.564   0.106   1.392
>>HETATM   15  C     2     2       0.779   0.380   0.903
>>HETATM   16  C     2     2       1.220   1.824   1.201
>>HETATM   17  N     2     2       2.587   2.069   0.782
>>
>>Output:
>>
>>[ moleculetype ]
>>; Name nrexcl
>> _2      3
>>
>>[ atoms ]
>>;   nr      type  resnr resid  atom  cgnr   charge     mass
>>     1        NL     1   _2     NAA     1    0.704  14.0067
>>     2         H     1   _2     HAA     1    0.059   1.0080
>>     3         H     1   _2     HAB     1    0.059   1.0080
>>     4         H     1   _2     HAC     1    0.059   1.0080
>>     5       CH2     1   _2     CAB     1    0.119  14.0270
>>     6       CH2     1   _2     CAC     2    0.119  14.0270
>>     7        NL     1   _2     NAD     2    0.704  14.0067
>>     8         H     1   _2     HAE     2    0.059   1.0080
>>     9         H     1   _2     HAF     2    0.059   1.0080
>>    10         H     1   _2     HAD     2    0.059   1.0080
>>
>>The queries to the output are :
>>
>>1)   The linker now has three hydrogens attached to nitrogen whereas the 
>>linker with the peptide will have only one hydrogen attached to
>>nitrogen.So can we restrict the number of hydrogens to one or should i now
>>delete two hydrogens from the topology file before using it for my
>>system????
>>
>>2)   Should I use the same parameters including the charges directly as
>>given in the output in the topology file for my simulation or are there
>>other issues to look into before using this topology file?????
>>
>>3)  These parameters were developed by the server for an isolated linker
>>(N-C-C-N).So can i use the same parameters for the linker when it is bound
>>to my peptide (XXX-Linker-XXX)????
>>
>>Please shed some light into this issue.
>>
>>Thanking all in advance.
>>                        Alok Jain
>>
>>
>>
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>>    
>>