[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
James Starlight
jmsstarlight at gmail.com
Wed Dec 12 12:54:15 CET 2012
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 ?
James
James
2012/12/12, James Starlight <jmsstarlight at gmail.com>:
> Also I've made the same parameters with the capped chromophore (NH2 on
> the C-term (instead of OH) and ACE on the N term (instead of H).
>
> When I've defined that chromophore as the Protein I've obtained an error
>
> Fatal error:
> Atom OXT in residue CRO 66 was not found in rtp entry CRO with 38 atoms
> while sorting atoms
>
> I've not found any OXT atoms in the residues in the RTP of other amino
> acids. Must that terminal oxygen be missing OH ( which I've replaced
> my ACE in my model) ? Where it should be defined ?
>
> James
>
>
> 2012/12/11, James Starlight <jmsstarlight at gmail.com>:
>> 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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>>
>
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