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

Wed Dec 12 15:42:40 CET 2012

Justin,

The IMPROPERS consisted of atom names (its correct as I understood).
The bond tern I've changed. The resulted RTP

[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
N    NC=O  -0.7301 6
CA1  CR     0.3611 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
O3   O=C   -0.5700 15
CA2  C=C    0.1854 16
CA3  CR     0.3611 17
C    C=O    0.5690 18
O    O=C   -0.5700 19
CB2  C=C   -0.1784 20
OH   OR    -0.5325 21
HA1  HCMM   0.0000 22
HA32 HCMM   0.0000 23
HA33 HCMM   0.0000 24
HD1  HCMM   0.1500 25
HD2  HCMM   0.1500 26
HE1  HCMM   0.1500 27
HE2  HCMM   0.1500 28
HG11 HCMM   0.0000 29
HG12 HCMM   0.0000 30
HG13 HCMM   0.0000 31
HOG1 HOR    0.4000 32
HB2  HCMM   0.1500 33
H11  HNCO   0.3700 34
HH   HOCC   0.4500 35
HB1  HCMM   0.0000 36
 [ bonds ]
HG11 CG1
HG12 CG1
CG1  HG13
CG1  CB1
OG1  HOG1
OG1  CB1
CB1  HB1
CB1  CA1
HE2  CE2
N    H11
N    CA1
HH   OH
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

That produce correct structure from my eGFP model :) But I suppose
that charges should be changed in accordance to the paper which you
provide me ( in my case charges were assigned by Swiss Param's
building blocks)

Thanks for help

James

2012/12/12, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 12/12/12 6:54 AM, James Starlight wrote:
>> Oh that problem was imperically resolved by renamind O2 ( which are
>> not terminal but pdb2gmx define them as a terminal ) atom to O3
>>
>> The only question about my chromophore is the definition of the IMPROPER
>> groups.
>> As I've posted above my initial model was CAPPED from C and N termi by
>> NH2 and Ace. The resulted topology consisted of Improper for bonds
>> between chromophore atoms and Capped groups ( e.g :
>>
>> With ACE (C-3 O-1 C-4 H-11 H-12 H-1 )
>> IMPH C    N1   CA3  O
>> IMPH N    C3   CA1  H11
>> IMPH C3   O1   N    C4
>> IMPH C4   HC11 C3   H1
>> IMPH C4   HC11 C3   H12
>>
>> With NH2  (N1-H2-H3)
>> IMPH N1   H2   C    H3
>> IMPH C    N1   CA3  O
>> That strings were removed from chromophore RTP. But in my final model
>> there are 2 amino acids insted of capped groups so the IPROPERS must
>> be inclusion for protein-chromophore nonds. How it could be done ?
>>
>> In some amino acids I've found -N and -C blocks that (if I understood
>> correctly) for C and N atoms of the adjacent residues. How that atoms
>> must be defined correctly in the protein-chromophore comples ?
>>
>
> + and - indicate next and previous residues, respectively.  Presumably your
>
> chromophore engages in the same types of peptide bonds as any other amino
> acid,
> so the syntax is the same as any other case.
>
> -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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