[gmx-users] Topology for hetroatom (PRODRG)

[Maik Goette]

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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