[gmx-users] sub: topology file error
kalai sivam
kalaiphysics.buc at gmail.com
Tue Jul 26 13:31:36 CEST 2016
dear gromacs user,
*i am a gromacs beginner. I have used OPLS-AA force field for
protein-ligand interaction.*
*I have created topology for ligand.. During energy minimisation
step, error occur.*
pls......can you help me... what the basic parameters must to do
topology..??
topology for my ligand:
*HETATM 1 N CME J 111 35.056 8.389 -65.732 1.00
12.85 N *
*HETATM 2 NH1 CME J 111 35.273 7.556 -66.261 1.00
12.85 H *
* HETATM 3 NH2 CME J 111 34.432 8.154 -64.974 1.00
12.85 H *
*HETATM 4 CA CME J 111 34.408 9.378 -66.615 1.00
12.72 C *
*HETATM 5 HA1 CME J 111 34.398 10.314 -66.056 1.00
12.72 H *
*HETATM 6 C CME J 111 33.008 8.939 -66.964 1.00
11.45 C *
*HETATM 7 HH11 CME J 111 32.489 8.990 -66.007 1.00
11.45 H *
* HETATM 8 HH12 CME J 111 32.663 9.596 -67.762 1.00
11.45 H *
*HETATM 9 O1 CME J 111 32.792 7.791 -67.335 1.00
11.90 O *
*HETATM 10 H1 CME J 111 32.660 7.226 -66.570 1.00
11.90 H *
*HETATM 11 CB CME J 111 35.171 9.597 -67.925 1.00
13.37 C *
*HETATM 12 HB1 CME J 111 35.062 8.718 -68.561 1.00
13.37 H *
*HETATM 13 HB2 CME J 111 36.226 9.759 -67.706 1.00
13.37 H *
*HETATM 14 SG CME J 111 34.519 11.018 -68.763 1.00
15.40 S *
*HETATM 15 SD CME J 111 35.658 11.048 -70.464 1.00
22.64 S *
*HETATM 16 CE CME J 111 34.703 10.137 -71.629 1.00
22.85 C *
*HETATM 17 HE1 CME J 111 34.910 10.506 -72.634 1.00
22.85 H *
*HETATM 18 HE2 CME J 111 33.644 10.263 -71.402 1.00
22.85 H *
*HETATM 19 CZ CME J 111 35.060 8.659 -71.549 1.00
25.41 C *
*HETATM 20 HZ1 CME J 111 36.050 8.540 -71.108 1.00
25.41 H *
* HETATM 21 HZ2 CME J 111 35.072 8.217 -72.546 1.00
25.41 H *
* HETATM 22 O CME J 111 34.078 8.011 -70.728 1.00
29.66 O *
* HETATM 23 H CME J 111 33.908 8.546 -69.949 1.00
29.66 H *
*These are errors:*
NOTE 1 [file em_real.mdp, line 20]:
em_real.mdp did not specify a value for the .mdp option "cutoff-scheme".
Probably it was first intended for use with GROMACS before 4.6. In 4.6,
the Verlet scheme was introduced, but the group scheme was still the
default. The default is now the Verlet scheme, so you will observe
different behaviour.
Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
NOTE 2 [file em_real.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 4229912197
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
ERROR 1 [file topol.top, line 64]:
No default Bond types
ERROR 2 [file topol.top, line 65]:
No default Bond types
ERROR 3 [file topol.top, line 69]:
No default Bond types
ERROR 4 [file topol.top, line 70]:
No default Bond types
ERROR 5 [file topol.top, line 76]:
No default Bond types
ERROR 6 [file topol.top, line 77]:
No default Bond types
ERROR 7 [file topol.top, line 141]:
No default Angle types
ERROR 8 [file topol.top, line 143]:
No default Angle types
ERROR 9 [file topol.top, line 144]:
No default Angle types
ERROR 10 [file topol.top, line 145]:
No default Angle types
ERROR 11 [file topol.top, line 152]:
No default Angle types
ERROR 12 [file topol.top, line 153]:
No default Angle types
ERROR 13 [file topol.top, line 154]:
No default Angle types
ERROR 14 [file topol.top, line 155]:
No default Angle types
ERROR 15 [file topol.top, line 156]:
No default Angle types
ERROR 16 [file topol.top, line 162]:
No default Angle types
ERROR 17 [file topol.top, line 164]:
No default Angle types
ERROR 18 [file topol.top, line 165]:
No default Angle types
ERROR 19 [file topol.top, line 166]:
No default Angle types
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