[gmx-users] sub: topology file error

Tue Jul 26 13:34:54 CEST 2016

On 7/26/16 7:31 AM, kalai sivam wrote:
> 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..??
>

A topology must define all interactions within a given molecule.  These are 
explained fully in Chapter 5 of the manual, and in concert with a thorough 
reading of the extensive OPLS-AA force field literature, you should gain an 
understanding of the work it will take to produce a correct topology.

The errors below suggest you are assigning bonded interactions that the force 
field doesn't know.  If the connectivity is correct, then you need to 
parametrize the missing terms, again referring to the OPLS-AA literature for the 
proper protocol.  Note that this is an advanced topic requiring considerable 
care and knowledge of the force field.

>
> topology for my ligand:
>

These are coordinates, not a topology.

-Justin

>
> *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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================