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

Wed Dec 12 11:18:39 CET 2012

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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>