[gmx-users] No default U-B types

[Justin Lemkul]

On 4/22/14, 2:31 AM, Shima Arasteh wrote:
> Hi all,
>
> There is an unnatural sidechain in my input file, so I added new lines as new-defined(DPP) residue to the .rtp and .hdb files.
> Also there were some missed bonds, angles, and dihedrals in generated .top file, which manually added in.
> When I go through the grompp to do EM, I find a fatal error about the new defined residue:
>
> No default U-B types
>
> As I checked this kind of angle, it exists in other residues such as lysine as well. This angle is (defined by atom types):
> CT1 CT2 NH3
>

That angle doesn't exist in other amino acids.  For lysine, CT2-CT2-NH3 exists, 
but not CT1-CT2-NH3.  You'll have to add parameters for this angle, and probably 
a few dihedrals, as well.

-Justin

>
> I checked the atom names, It seems ok.
>
> Part of the top file is as follow:
>
>   residue   1 DPP rtp DPP  q +2.0
>       1        NH3      1    DPP      N      1       -0.3     14.007   ; qtot -0.3
>       2         HC      1    DPP     H1      2       0.33      1.008   ; qtot 0.03
>       3         HC      1    DPP     H2      3       0.33      1.008   ; qtot 0.36
>       4         HC      1    DPP     H3      4       0.33      1.008   ; qtot 0.69
>       5        CT1      1    DPP     CA      5       0.21     12.011   ; qtot 0.9
>       6         HB      1    DPP     HA      6        0.1      1.008   ; qtot 1
>       7        CT2      1    DPP     CB      7       0.21     12.011   ; qtot 1.21
>       8         HA      1    DPP    HB1      8       0.05      1.008   ; qtot 1.26
>       9         HA      1    DPP    HB2      9       0.05      1.008   ; qtot 1.31
>      10        NH3      1    DPP     NG     10       -0.3     14.007   ; qtot 1.01
>      11         HC      1    DPP    HG1     11       0.33      1.008   ; qtot 1.34
>      12         HC      1    DPP    HG2     12       0.33      1.008   ; qtot 1.67
>      13         HC      1    DPP    HG3     13       0.33      1.008   ; qtot 2
>      14          C      1    DPP      C     14       0.51     12.011   ; qtot 2.51
>      15          O      1    DPP      O     15      -0.51     15.999   ; qtot 2
>
> Fatal error:
> ERROR 1 [file topol.top, line 853]:
>    No default U-B types
>
> line 853:     5     7    10     5
>
>
>
> Would you please let me your suggestions about the reason of this error? How can I pass it? Would you please help me?
>
> Thanks in advance for your suggestions.
>
> Sincerely,
> Shima
>

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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