[gmx-users] Topology for hetroatom (PRODRG)

[Alok]

Thanks Maik,
    
But as david sugged me that i have to include topology of my linker in 
rtp file , so now i am not using PRODRG server.
I also find the option for fixing the optimal no of Hydrogen in PRODRG.
It is DELHYD "atom name" flag above the PDB file.
Thanks again for ur suggesion.
                                
       Alok Jain
                     
Maik Goette wrote:

> Hi
>
> I had similar problems longer time ago.
> PRODRG seems to guess the optimal no of hydrogens.
> But you are able to tell the PRODRG-Server to don't place specific 
> hydrogens.
> How it works is listed in a howto on the servers homepage.
> I preferred ASCII-Input, so I am not sure how to include this option 
> into PDB. This may also occur in the "manual".
>
> Concerning the charges, one has to pay attention, that the charges may 
> change significantly, depending on what atom will be attached to the 
> linkers nitrogen. This might even influence the AA on the opposite side.
>
> A possible solvation may be, to change the linker into glycins.
>
> The other way would be a QM of the linker, I guess.
>
> Regards
>
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel.  : ++49 551 201 2310
> Fax   : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
>         mgoette2[at]gwdg.de
> WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> 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..
>>                   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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>> .
>>
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