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

Sat Dec 15 19:34:51 CET 2012

The last problem with which I've forced during preparation of my
chromophore is when I've defined bond between chromophore and the next
residue

C    +N

That produce 15 addition errors about unknown UB and dihedral types
in the atoms of the next residue (not in the chromophore) where all UB
and impropers must be defined initially.
Why that occurs ?

James

2012/12/14, James Starlight <jmsstarlight at gmail.com>:
> 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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>