Thank you Dr. Alessandra
I actually generated topologies for my ligands using charmm server
generated itp files had few overriding names, which are throwing errors
when combined.
Please have a look at the itp files pasted here.
...........................................................................................................................
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
CG2O6 6 12.0110 0.600 A 3.56359487256e-01
2.928800e-01
HGP1 1 1.0080 0.340 A 4.00013524445e-02
1.924640e-01
NG2S2 7 14.0070 -0.690 A 3.29632525712e-01
8.368000e-01
OG2D1 8 15.9994 -0.580 A 3.02905564168e-01
5.020800e-01 ; 2.49451641079e-01 5.020800e-01
[ bondtypes ]
; i j func b0 Kb
CG2O6 NG2S2 1 1.360000e-01 3.598240e+05
CG2O6 OG2D1 1 1.230000e-01 5.439200e+05
NG2S2 HGP1 1 1.000000e-01 4.016640e+05
[ pairtypes ]
; i j func sigma1-4 epsilon1-4
CG2O6 OG2D1 1 3.02905564168e-01 3.83469934154e-01
HGP1 OG2D1 1 1.44726496762e-01 3.10857403193e-01
NG2S2 OG2D1 1 2.89542083396e-01 6.48182492821e-01
OG2D1 OG2D1 1 2.49451641079e-01 5.02080000000e-01
[ angletypes ]
; i j k func th0 cth S0 Kub
CG2O6 NG2S2 HGP1 5 1.2000000e+02 4.1840000e+02 0.0000000e+00
0.0000000e+00
HGP1 NG2S2 HGP1 5 1.2000000e+02 1.9246400e+02 0.0000000e+00
0.0000000e+00
NG2S2 CG2O6 NG2S2 5 1.1500000e+02 5.8576000e+02 0.0000000e+00
0.0000000e+00
NG2S2 CG2O6 OG2D1 5 1.2250000e+02 6.2760000e+02 2.3700000e-01
4.1840000e+04
[ dihedraltypes ]
; i j k l func phi0 cp mult
NG2S2 CG2O6 NG2S2 HGP1 9 1.800000e+02 6.276000e+00 2
OG2D1 CG2O6 NG2S2 HGP1 9 1.800000e+02 5.857600e+00 2
[ dihedraltypes ]
; i j k l func q0 cq
CG2O6 NG2S2 NG2S2 OG2D1 2 0.000000e+00 6.694400e+02
............................................................................................................................
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
HGP1 1 1.0080 0.369 A 4.00013524445e-02
1.924640e-01
NG2D1 7 14.0070 -0.370 A 3.29632525712e-01
8.368000e-01
OG2D1 8 15.9994 0.001 A 3.02905564168e-01
5.020800e-01 ; 2.49451641079e-01 5.020800e-01
[ bondtypes ]
; i j func b0 Kb
NG2D1 HGP1 1 1.000000e-01 3.807440e+05
NG2D1 OG2D1 1 1.225000e-01 4.853440e+05
[ pairtypes ]
; i j func sigma1-4 epsilon1-4
HGP1 OG2D1 1 1.44726496762e-01 3.10857403193e-01
NG2D1 OG2D1 1 2.89542083396e-01 6.48182492821e-01
OG2D1 OG2D1 1 2.49451641079e-01 5.02080000000e-01
[ angletypes ]
; i j k func th0 cth S0 Kub
OG2D1 NG2D1 HGP1 5 1.1300000e+02 4.1003200e+02 0.0000000e+00
0.0000000e+00
....................................................................................................................................
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14
HGP1 1 1.0080 0.500 A 4.00013524445e-02
1.924640e-01
OG311 8 15.9994 -0.500 A 3.14487247504e-01
8.037464e-01
[ bondtypes ]
; i j func b0 Kb
OG311 HGP1 1 9.600000e-02 4.560560e+05
OG311 OG311 1 1.420000e-01 3.581504e+05
[ angletypes ]
; i j k func th0 cth S0 Kub
OG311 OG311 HGP1 5 1.0150000e+02 5.0208000e+02 0.0000000e+00
0.0000000e+00
[ dihedraltypes ]
; i j k l func phi0 cp mult
HGP1 OG311 OG311 HGP1 9 0.000000e+00 7.531200e-01 3
..................................................................................................................................
I just combined files into my system itp file (solvated membrane protein)
Can i simulate these three molecules together?
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
