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

[Justin Lemkul]

On 12/14/12 11:42 PM, James Starlight wrote:
> The topology with the below params produced that 118 errors during
> grompp processings ( after pdb2gmx processing the geoetry of the
> mollecule was correct )
>
> [CRN]
>   [ atoms ]
> CG2  CA    -0.0900 0
> CD1  CA    -0.0800 1
> CD2  CA    -0.0800 2
> CE1  CA    -0.2800 3
> CE2  CA    -0.2800 4
> CZ   CA     0.4500 5
> N    NH1   -0.4700 6
> CA1  CPH1   0.1000 7
> CB1  CT1   -0.1400 8
> CG1  CT3    0.0900 9
> OG1  OH1   -0.6600 10 ;!-0.6800
> C1   CPH2   0.5000 11
> N2   NR2   -0.6000 12
> N3   NR1   -0.5700 13
> C2   CPH1   0.5700 14
> O3   O     -0.5700 15
> CA2  CPH1   0.1000 16
> CA3  CPH1    0.1000 17
> C    C      0.5100 18
> O    O     -0.5100 19
> CB2  CE1   -0.1400 20
> OH   O     -0.6200 21
> HA1  HB     0.0700 22
> HA32 HB     0.0700 23
> HA33 HB     0.0700 24
> HD1  HP     0.1400 25
> HD2  HP     0.1400 26
> HE1  HP     0.1000 27
> HE2  HP     0.1000 28
> HG11 HA     0.0900 29
> HG12 HA     0.0900 30
> HG13 HA     0.0900 31
> HOG1 H      0.4300 32
> HB2  HA1    0.2100 33
> H11  H      0.3700 34
> HB1  HA1    0.2100 36
>   [ bonds ]
> HG11 CG1
> HG12 CG1
> CG1  HG13
> CG1  CB1
> OG1  HOG1
> OG1  CB1
> CB1  HB1
> CB1  CA1
> HE2  CE2
> N    H11
> N    CA1
> CA1  HA1
> CA1  C1
> CE2  CD2
> CE2  CZ
> HD2  CD2
> OH   CZ
> CD2  CG2
> CZ   CE1
> N2   C1
> N2   CA2
> C1   N3
> HA33 CA3
> CG2  CB2
> CG2  CD1
> CE1  HE1
> CE1  CD1
> CA2  CB2
> CA2  C2
> N3   CA3
> N3   C2
> CB2  HB2
> CA3  C
> CA3  HA32
> CD1  HD1
> C2   O3
> C    O
>
>   [ impropers ]
> CG2  CD1  CB2  CD2
> CD1  CE1  CG2  HD1
> CD2  CE2  CG2  HD2
> CE2  CZ   CD2  HE2
> CB2  CA2  CG2  HB2
> CA2  N2   CB2  C2
> C1   CA1  N2   N3
> CA1  N    C1   CB1
> CA1  CB1  C1   HA1
> CB1  OG1  CA1  CG1
> CB1  CG1  CA1  HB1
> C2   N3   CA2  O3
> N3   C2   C1   CA3
> CA3  C    N3   HA33
> CA3  HA33 N3   HA32
> CZ   CE1  CE2  OH
> CE1  CZ   CD1  HE1
> CG1  HG11 CB1  HG12
> CG1  HG11 CB1  HG13
> ; with next residue
> C    +N   CA3  O
> ; with previous residue
> N    -C   CA1  H11
> [ cmap ]
> -C  N  CA1  C1  N2
> CA2 C2 N3 CA3 C
>
> The only in that I not sure in that model is the corrections in the
> cmap.itp which I added (I've used first two terms which are correspond
> to the backbone atoms of the standart amino acid:
> C NH1 CT1 C NH1 1 24 24\
> C NH1 CT1 C N 1 24 24\
>   and renamed it to the chromophore atom names)
>
> by the way If you had had your rtp of the chromophore which you've
> done in accordance to that paper could you provide me with them for
> comparison with my model ?
>

I gave the files to our collaborators some time ago and archived my own copies. 
  I don't have immediate access to them, sorry.

-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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