[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
James Starlight
jmsstarlight at gmail.com
Sat Dec 15 20:18:39 CET 2012
So as I understood it've happened because the conformation of the
adjacent residue is differ when that residue bounded to the
chromophore ( in comparison to the residue in unbound capped form).
But in term of the backbone geometry of C and N-terms chromophore is
like a typical amino acid. Also Chromophore is defined as a protein in
the residue.dat. When I've examined error log of my system I've
noticed that missing UB and dihedral parametrs of the i+1 residue have
never present in the ffbounded.itp ( the exact combination of the
triplet and quadruplet of atoms for UB and dihedral). Is there any
other ways to define termi of my non standard residue as the standard
one?
James
2012/12/15, Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>>>>
>>>> ========================================
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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