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

[James Starlight]

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 ?


James

2012/12/14, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 12/14/12 3:20 PM, James Starlight wrote:
>> Justin,
>>
>> in the case of the system with the atom types assigned from that paper
>> the grompp produced above 118 errors of non standard bond, angle as
>> well as dihedral types ;o So it' seems that some 118 addition terms
>> must be added to the ffbonded.itp to the existing charmm parameters(
>> it's uncommon for me because in that case the atom names werefrom
>> standart charmm ff but the total number of errors was bigger than in
>> case of Swiss params non-standart names usage).
>>
>
> I'm not sure why there were so many errors when you used those parameters.
> Like
> I said, we've used them before.  I recall a few errors along the way, but
> manual
> assignment of the bonded parameters according to the paper is fairly
> straightforward.
>
>> By the way I've simulated choromophore produced by SWISS ( with the
>> charges assigned from the paper) in the vacuum and didnt notice any
>> inaccuracy in the conformation of chromophore. So the last that I
>> should is the carefull assignment of the 9 missed dihedral terms with
>> the rest of the protein.
>>
>
> Sounds like a reasonably approach.  Good luck.
>
> -Justin
>
> --
> ========================================
>
> 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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