[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
James Starlight
jmsstarlight at gmail.com
Wed Dec 12 06:37:18 CET 2012
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).
James
2012/12/11, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 12/11/12 4:13 PM, James Starlight wrote:
>> Today I've made parametrization of the chromophore group by means of
>> Swiss param and integrated that topology into charmm27 ff. The only
>> problem that I have is with the N-term N atom of the chromophore. It's
>> likely that I made mistake to parametrize it into full protonated form
>> (NH2).
>>
>
> Protonation states of termini can indeed cause problems. Model compounds
> often
> use capping groups (methyl, acetyl, etc) to mitigate these effects. You can
>
> probably get some tips from http://pubs.acs.org/doi/abs/10.1021/jp014476w,
> or
> otherwise just use their parameters.
>
>> When I've used pdb2gmx on the GFP structure the peptide bond between
>> that N atom and adjacent O ( from C term of adjacent residue) is
>> incorrect ( both oxygens preserves on the C atom so my system had
>> divided onto 2 chains as well as had incorrect charge). How I could
>> define the N atom in the topology as the N-terminal? (I've delited
>> both hydrogens from RTP as well as from HDB files but the problem
>> didn’t resolved. Also I'm using -ignh on the input pdb to ignore all
>> hydrogens from the model)
>>
>
> Copying and pasting your .rtp and .hdb entries would help. Also note that
> the
> chromophore needs to be defined as protein in residuetypes.dat, otherwise
> the
> protein chain will terminate erroneously and you'll get protonation state
> problems.
>
> -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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