[gmx-users] Topology for hetroatom (PRODRG)

[Alok]

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