[gmx-users] add parameter

Malihe Hasanzadeh ml.hasanzadeh at gmail.com
Thu Feb 11 18:03:49 CET 2016

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

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?

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