[gmx-users] topology file from glycam/gaff to gromacs

[Rasha Alqus]

Dear Gromacs user ,



i am a new user to gromacs and i am planning to run an MD for sugar system with nanoatoms in gromacs, i will use glycame force field for sugar and gaff force field for the other, I have the following question about the topology file:



1-i produced the top file that is compatible to gromacs and i want to ask



this is the top of the topology file, i will use 1-4 scale which is 1 as my reach requirement, but I need to include the force field line which come after these line,

;[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
; 1 2 no 1 1



1-since am using glycam and gaff where to get the ffglycam.itp as well as gaff.itp to include them in the top file.

2-i used amb2gmx.pl to produce the top file, should i do them as individual first them combine them, or i can use the files that have both my systems togather and then use amb2gmx.pl





thank you for the help in advance

rasha alqus



 x.top created by rdparm2gmx.pl Thu Mar 19 13:54:18 GMT 2015

;[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
;  1             2               no             1     1

[ atomtypes ]
;name  bond_type    mass    charge   ptype          sigma      epsilon
H1            H1      0.0000  0.0000  A   2.47135e-01  6.56888e-02
Ho            Ho      0.0000  0.0000  A   3.56359e-02  1.25520e-01
ha            ha      0.0000  0.0000  A   2.59964e-01  6.27600e-02
H2            H2      0.0000  0.0000  A   2.29317e-01  6.56888e-02
Os            Os      0.0000  0.0000  A   3.00001e-01  7.11280e-01
ca            ca      0.0000  0.0000  A   3.39967e-01  3.59824e-01
Cg            Cg      0.0000  0.0000  A   3.39967e-01  4.57730e-01
Oh            Oh      0.0000  0.0000  A   3.06647e-01  8.80314e-01

[ moleculetype ]
; Name            nrexcl
  x                      3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB
     1         Ho      1    ROH    HO1      1    0.44500   1.000000
     2         Oh      1    ROH     O1      2   -0.63900  16.000000
     3         Cg      2    0GB     C1      3    0.38400  12.000000
     4         H2      2    0GB     H1      4    0.00000   1.000000
     5         Os      2    0GB     O5      5   -0.47100  16.000000
     6         Cg      2    0GB     C5      6    0.22500  12.000000
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    28         ca      3    GRA    C3A     28    0.00000  12.000000
    29         ca      3    GRA    C4A     29    0.00000  12.000000
    30         ca      3    GRA    C5A     30    0.00000  12.000000
    31         ca      3    GRA    C6A     31    0.00000  12.000000
    32         ca      3    GRA    C7A     32    0.00000  12.000000
    33         ca      3    GRA    C8A     33    0.00000  12.000000
    34         ca      3    GRA    C9A     34    0.00000  12.000000
    35         ca      3    GRA    C0B     35    0.00000  12.000000
    36         ca      3    GRA    C1B     36    0.00000  12.000000
    37         ca      3    GRA    C2B     37    0.00000  12.000000
    38         ca      3    GRA    C3B     38    0.00000  12.000000
.....