[gmx-users] Topology for hetroatom (PRODRG)

[David]

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
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++