[gmx-users] topology error

[Justin Lemkul]

On 8/19/16 8:05 AM, kalai sivam wrote:
> dear, all gromacs user
>  i have to assign the co-ordinate to create the topology.
>  from your suggestion , I  include the missing parameters...
> but still one error i can't rectify..
>
>
> say some information about the co-ordinate file...
>
>
> *My parameters are:*
>
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
> ; residue 111 CME rtp CME  q +0.5
>      1   opls_238    111    CME      N      1       -0.5    14.0067   ;
> qtot -0.5
>      2   opls_241    111    CME    NH1      1       0.23      1.008   ;
> qtot -0.27
>      3   opls_241    111    CME    NH2      1       0.27      1.008   ;
> qtot 0
>      4   opls_206    111    CME     CA      2      -0.18     12.011   ;
> qtot -0.18
>      5   opls_140    111    CME    HA1      2       0.18      1.008   ;
> qtot 0
>      6   opls_157    111    CME      C      3      0.145     12.011   ;
> qtot 0.145
>      7   opls_140    111    CME   HH11      3       0.06      1.008   ;
> qtot 0.205
>      8   opls_140    111    CME   HH12      3       0.06      1.008   ;
> qtot 0.265
>      9   opls_154    111    CME    OH1      3      0.683    15.9994   ;
> qtot 0.948
>     10   opls_155    111    CME    HO1      3     -0.418      1.008   ;
> qtot 0.53
>     11   opls_214    111    CME     CB      4     0.0975     12.011   ;
> qtot 0.6275
>     12   opls_140    111    CME    HB1      4       0.06      1.008   ;
> qtot 0.6875
>     13   opls_140    111    CME    HB2      4       0.06      1.008   ;
> qtot 0.7475
>     14   opls_208    111    CME     SG      4    -0.2175     12.011   ;
> qtot 0.53
>     15   opls_210    111    CME     SD      5    -0.2175     12.011   ;
> qtot 0.3125
>     16   opls_206    111    CME     CE      5     0.0975     12.011   ;
> qtot 0.41
>     17   opls_140    111    CME    HE1      5       0.06      1.008   ;
> qtot 0.47
>     18   opls_140    111    CME    HE2      5       0.06      1.008   ;
> qtot 0.53
>     19   opls_157    111    CME     CZ      6      0.145     12.011   ;
> qtot 0.675
>     20   opls_140    111    CME    HZ1      6       0.06      1.008   ;
> qtot 0.735
>     21   opls_140    111    CME    HZ2      6       0.06      1.008   ;
> qtot 0.795
>     22   opls_154    111    CME     OH      6     -0.683    15.9994   ;
> qtot 0.112
>     23   opls_155    111    CME     HO      6      0.418      1.008   ;
> qtot 0.53
>
>
>
> * Error has been:*
>
>
>
> *ERROR 1 [file topol.top, line 178]:   No default Ryckaert-Bell. types*
>
>
> NOTE 1 [file topol.top, line 242]:
>   System has non-zero total charge: 0.530000
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
>
>  please, say some clarification..
>

Your net charge is physically unreasonable, so start by assigning proper charges.

For the missing dihedral, check that you are using correct atom types for the 
missing interaction and reassign them if you are not.  If the types are correct, 
then you need to parametrize the missing dihedral in a manner consistent with 
the parent force field.  For OPLS, this means a 1-dimensional QM potential 
energy scan to which you fit the necessary dihedral term(s).

-Justin

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

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

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