[gmx-users] add parameter

[Malihe Hasanzadeh]

Hi
I have three water molecules and one new residue that I want to add their
parameters to force field Amber99sb. One of water molecules has only one
hydrogen, and since I want to prevent from replacing with SOL in solvation
step, So I define them as new residue in .rtp file:

[ INN ]
 [ atoms ]
   H1    H           0.384620     1
    O    O          -0.671930     2
   H2    H           0.384620     3


[ INT ]
 [ atoms ]
   H1    H           0.286310     1
    O    O          -0.341910     2
   H2    H           0.286310     3


[ INB ]
 [ atoms ]
   H1    H           0.477860     1
    O    O          -1.092580     2
Also define them in .dat file as Protein  and in .hdb file as below:

INN    2
1    7    H1    O
1    7    H2    O
INT    2
1    7    H1    O
1    7    H2    O
INB    1
1    7    H1    O

But when I start MD simulation(gromacs 5.0.4) in step of mdrun ...em,
gives segmentation fault! when I remove their parameters in .hdb file, it
is done but without any hydrogen for them, just three oxygen atoms in
em.gro!

Also I have another problem with that new residue, this residue is like a
Lys but has two carbonyl groups binded to extra carbon instead of amino
group in Lys. So I used Lys parameters for that and add some bonds and
atoms to it:

[ NEW ] ;
 [ atoms ]
    N       N
    H       H
   CA       CT
   HA        H1
   CB       CT
  HB1       HC
  HB2       HC
   CG      CT
  HG1      H
  HG2      H
   CD      CT
  HD1      HC
  HD2      HC
   CE      CT
  HE1      HP
  HE2      HP
   NZ      N
   HZ      H
   CX      C
  OQ1     O
  OQ2     O
    C      C
    O      O
 [ bonds ]
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB1
    CB   HB2
    CB    CG
    CG   HG1
    CG   HG2
    CG    CD
    CD   HD1
    CD   HD2
    CD    CE
    CE   HE1
    CE   HE2
    CE    NZ
    NZ    HZ
    NZ    CX
     C     O
    CX   OQ1
    CX   OQ2
 [ impropers ]
    -C    CA     N     H
    CA    +N     C     O
when I added only atoms parameters in .rtp file, finally in em.gro file
there wasn't any bond between atoms of new residue and when I added bond
parameters also, in grompp gives 10 error about "default angel and
dihedral"! I find the number of angels in .top file and added them to
ffbonded.itp, but anything have no change.
please help me. what is my mistake about these two insistent problems?
Thanks
Malihe