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

Sat Dec 15 19:42:17 CET 2012

On 12/15/12 1:34 PM, James Starlight wrote:
> 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 ?
>

Because the combinations of parameters don't exist in ffbonded.itp.

-Justin

> 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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>>

-- 
========================================

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

========================================