[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[Justin Lemkul]

On 12/12/12 12:37 AM, James Starlight wrote:
> That the mollecule that I made
>
> [ CRO ]
>   [ atoms ]
> CG2   CB      0.0284 0
> CD1   CB     -0.1500 1
> CD2   CB     -0.1500 2
> CE1   CB     -0.1500 3
> CE2   CB     -0.1500 4
> CZ    CB      0.0825 5
> HL    H       0.3600 39
> NR    NH1    -0.9900  6
> CA1   CR      0.3310 7
> CB1   CR      0.2800 8
> CG1   CR      0.0000 9
> OG1   OR     -0.6800 10
> C1    C=O     0.4490 11
> N2    N=C    -0.6210 12
> N3    NC=O   -0.4201 13
> C2    C=O     0.6156 14
> O2    O=C    -0.5700 15
> CA2   C=C     0.1854 16
> CA3   CR      0.3611 17
> C     C=O     0.6590 18
> O3    O=C    -0.5700 19
> CB2   C=C    -0.1784 20
> OH    OR     -0.5325 21
> HA1   HCMM    0.0000 22
> HB1   HCMM    0.0000 23
> HA32  HCMM    0.0000 24
> HA33  HCMM    0.0000 25
> HD1   HCMM    0.1500 26
> HD2   HCMM    0.1500 27
> HE1   HCMM    0.1500 28
> HE2   HCMM    0.1500 29
> HH    HOCC    0.4500 30
> HG11  HCMM    0.0000 31
> HG12  HCMM    0.0000 32
> HG13  HCMM    0.0000 33
> HOG1  HOR     0.4000 34
> HB2   HCMM    0.1500 35
> OH    OR     -0.6500 36
> H1    HOCO    0.5000 37
>
>   [ bonds ]
> HCMM CR
> CR   CR
> OR   HOR
> OR   CR
> HCMM CB
> HL   NR
> NH1  CR
> HOCC OR
> CR   C=O
> CB   CB
> OR   CB
> N=C  C=O
> N=C  C=C
> C=O  NC=O
> CB   C=C
> C=C  C=C
> C=C  C=O
> NC=O CR
> HOCO OR
> C=C  HCMM
> OR   C=O
> C=O  O=C
>   [ impropers ]
> CG2  CD1  CB2  CD2
> CD1  CE1  CG2  HD1
> CD2  CE2  CG2  HD2
> CE2  CZ   CD2  HE2
> CB2  CA2  CG2  HB2
> CA2  C2   CB2  N2
> C1   CA1  N2   N3
> CA1  CB1  C1   NR
> CA1  CB1  C1   HA1
> CB1  OG1  CA1  CG1
> CB1  CG1  CA1  HB1
> C2   N3   CA2  O2
> N3   C2   C1   CA3
> CA3  C    N3   HA33
> CA3  HA33 N3   HA32
> C    OH   CA3  O3
> CZ   CE1  CE2  OH
> CE1  CZ   CD1  HE1
> NR   C1   CA1 HL
>
> CRO    14
> 3       4       HG1     CG1     CB1	CA1
> 1       5       HB1     CB1     CA1	OG1     CG1
> 1       2       HOG1    OG1     CB1	CA1
> 1       5       HA1     CA1     NR	C1	CB1
> 1       2       H1      OH      C       O3
> 1       1       HL      NR      C1      CA1
> 1       6       HA32    CA3     C	N3
> 1       6       HA33    CA3     C	N3
> 1       1       HB2     CB2     CG2	CA2
> 1       1       HD1     CD1     CG2	CE1
> 1       1       HD2     CD2     CG2     CE2
> 1       1       HE1     CE1     CD1	CZ
> 1       1       HE2     CE2     CD2	CZ
> 1       2       HH      OH      CZ	CE1
>
>
> The only proble which I've forced with is in the N-term and
> non-integer charge ( 0.290).
>

You have another serious problem, in that your [bonds] and [impropers] 
directives specify atom types instead of names.  There's no way that can work.

Why not use standard backbone charges that are shared by all amino acids in 
CHARMM?  All the residues are the same with respect to the backbone.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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