Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds
Vitaly V. Chaban
vvchaban at gmail.com
Fri Feb 5 21:40:52 CET 2010
Yes, I provided all the possible entries in the N2T.although the
problem is the same. I also recreated PDB and re-measured the
distances but everything seems pretty correct in my PDB.
N N 2 S 0.17 S 0.17
F F 1 C 0.14
S S 4 O 0.17 O 0.17 C 0.18 N 0.17
C C 4 F 0.14 F 0.14 F 0.14 S 0.18
O O 1 S 0.17
Vitaly
On Fri, Feb 5, 2010 at 10:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>
>>> Vitaly V. Chaban wrote:
>>>>
>>>> In this context, it is interesting how X2TOP decides that two atoms
>>>> are connected? Only on the base of N2T: if the atom should have 4
>>>> neighbours, it looks for the appropriate number of them?
>>>>
>>> That's correct.
>>
>>
>> Then the interesting error is:
>> "Fatal error:
>> No forcefield type for atom C (1) with 0 bonds"
>>
>> while PDB contains other atoms than carbon. If it looks for neighbours
>> why does not it find them...
>>
>
> The error is complaining that atom 1 (a carbon atom) is not within searching
> distance of any atoms to which it should be bonded. Have you specified .n2t
> entries for every one of your atoms? For example, it is insufficient to
> specify an .n2t line for the central S (in your original post) and expect
> x2top to understand that the O, N, and C atoms to which it is connected can
> have their atom types determined. You need .n2t entries for all of those
> atoms, too, specifying that they are, in turn, connected to S in some way.
> The above error suggests that x2top is finding a carbon atom that you have
> not defined in the .n2t file.
>
> -Justin
>
>>
>>
>>
>>>> In my case, maybe it considers that 0.18 nm is too much for two atoms
>>>> to be connected?
>>>>
>>> The length defined in the .n2t file should be the actual bond length
>>> (from
>>> the coordinate file) +/- 10%, like specbond.dat, if I recall; x2top
>>> should
>>> not arbitrarily try to dictate that a bond is too long.
>>>
>>> -Justin
>>>
>>>> ---------- Forwarded message ----------
>>>> From: Vitaly V. Chaban <vvchaban at gmail.com>
>>>> Date: Fri, Feb 5, 2010 at 7:56 PM
>>>> Subject: Re: [gmx-users] Re: x2top and bonds. No forcefield type for
>>>> atom S (2) with 3 bonds
>>>> To: jalemkul at vt.edu, gmx-users at gromacs.org
>>>>
>>>>
>>>> Yes. This worked even with my N2T. I will probably recreate my PDB...
>>>>
>>>>
>>>> On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul <jalemkul at vt.edu>
>>>> wrote:
>>>>>
>>>>> Vitaly V. Chaban wrote:
>>>>>>
>>>>>> Justin,
>>>>>>
>>>>>> Am I correct that X2TOP uses only N2T file to make a topology?
>>>>>>
>>>>> Yes.
>>>>>
>>>>>> I made the full line for Sulphur but it didn't change the situation.
>>>>>> It looks strange that X2TOP notices 3 bonds although I propose to have
>>>>>> 4 bonds (and they are present). If I propose 3 bonds, it readily gives
>>>>>> an output... This is like it has predefined Sulphur with 3 bonds.
>>>>>>
>>>>> Certainly not. Take, for example, a simple SO4 molecule:
>>>>>
>>>>> REMARK
>>>>> HETATM 1 OAC DRG 1 5.850 14.800 -12.770 1.00 20.00
>>>>> O
>>>>> HETATM 2 SAE DRG 1 4.810 15.780 -12.710 1.00 20.00
>>>>> S
>>>>> HETATM 3 OAD DRG 1 3.550 15.150 -12.980 1.00 20.00
>>>>> O
>>>>> HETATM 4 OAB DRG 1 4.770 16.390 -11.340 1.00 20.00
>>>>> O
>>>>> HETATM 5 OAA DRG 1 5.070 16.850 -13.730 1.00 20.00
>>>>> O
>>>>>
>>>>> The topology is generated just fine with this .n2t file:
>>>>>
>>>>> S S 0 32.06 4 O 0.145 O 0.145 O 0.145 O 0.145
>>>>> O OM 0 15.9994 1 S 0.145
>>>>>
>>>>> I don't know what might be going on with your system, but I would
>>>>> suggest
>>>>> creating an .n2t file with only entries pertinent to your system, for
>>>>> all
>>>>> atoms involved. This is, of course, only really useful for debugging,
>>>>> since
>>>>> in theory, x2top should be easily extensible by appending the .n2t
>>>>> file.
>>>>>
>>>>> -Justin
>>>>>
>>>>>> Vitaly
>>>>>>
>>>>>>
>>>>>> On Fri, Feb 5, 2010 at 7:18 PM, Vitaly V. Chaban <vvchaban at gmail.com>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> This can be the reason when X2TOP gives the following error:
>>>>>>> "
>>>>>>> Fatal error:
>>>>>>> No forcefield type for atom S (2) with 3 bonds
>>>>>>> "
>>>>>>> ?
>>>>>>>
>>>>>>> I try to translate PDB of the TFSA anion
>>>>>>> O O
>>>>>>> || ||
>>>>>>> F3C-S-N-S-CF3
>>>>>>> || ||
>>>>>>> O O
>>>>>>>
>>>>>>> into topology.
>>>>>>>
>>>>>>>
>>>>>>> My PDB contains optimized geometry:
>>>>>>> HEADER TFSA
>>>>>>> COMPND TFSA
>>>>>>> AUTHOR VVC
>>>>>>> ATOM 1 N TFS 1 -0.000 0.444 -0.008 1.00 0.00
>>>>>>> ATOM 2 S TFS 1 1.401 -0.440 -0.189 1.00 0.00
>>>>>>> ATOM 3 S TFS 1 -1.400 -0.438 0.189 1.00 0.00
>>>>>>> ATOM 4 O TFS 1 -1.236 -1.810 -0.833 1.00 0.00
>>>>>>> ATOM 5 O TFS 1 -1.284 -1.009 1.805 1.00 0.00
>>>>>>> ATOM 6 O TFS 1 1.293 -1.026 -1.800 1.00 0.00
>>>>>>> ATOM 7 O TFS 1 1.233 -1.803 0.845 1.00 0.00
>>>>>>> ATOM 8 C TFS 1 -2.837 0.628 -0.107 1.00 0.00
>>>>>>> ATOM 9 C TFS 1 2.836 0.630 0.105 1.00 0.00
>>>>>>> ATOM 10 F TFS 1 -3.996 -0.097 0.093 1.00 0.00
>>>>>>> ATOM 11 F TFS 1 -2.805 1.094 -1.408 1.00 0.00
>>>>>>> ATOM 12 F TFS 1 -2.807 1.698 0.766 1.00 0.00
>>>>>>> ATOM 13 F TFS 1 2.802 1.099 1.404 1.00 0.00
>>>>>>> ATOM 14 F TFS 1 2.803 1.698 -0.771 1.00 0.00
>>>>>>> ATOM 15 F TFS 1 3.996 -0.093 -0.093 1.00 0.00
>>>>>>> END
>>>>>>>
>>>>>>> and my n2t file is
>>>>>>>
>>>>>>> C C 1 C ; CNT Carbon with one bond
>>>>>>> C C 2 C C : CNT double bonded Carbon
>>>>>>> O O 1 C ; CARBONYL OXYGEN (C=O)
>>>>>>> O OM 1 C ; CARBOXYL OXYGEN (CO-)
>>>>>>> O OA 2 C H ; HYDROXYL OXYGEN (OH)
>>>>>>> O OW 2 H H ; WATER OXYGEN
>>>>>>> N N 3 H C C ; PEPTIDE NITROGEN (N OR NH)
>>>>>>> N NT 3 H H C ; TERMINAL NITROGEN (NH2)
>>>>>>> N NL 4 C H H H ; TERMINAL NITROGEN (NH3)
>>>>>>> N NR5 2 C C ; AROMATIC N (5-RING,2 BONDS)
>>>>>>> N NR5* 3 C C H ; AROMATIC N (5-RING,3 BONDS)
>>>>>>> N NP 3 C C FE ; PORPHYRIN NITROGEN
>>>>>>> C C 3 C O * ; BARE CARBON (PEPTIDE,C=O,C-N)
>>>>>>> ; Note that order is importante here because of wildcards.
>>>>>>> C C3 4 H H H * ; ALIPHATIC CH3 GROUP
>>>>>>> C C2 4 H H C * ; ALIPHATIC CH2 GROUP
>>>>>>> C C1 4 H C * * ; ALIPHATIC CH GROUP
>>>>>>> C CB 3 C C C ; BARE CARBON (5-,6-RING)
>>>>>>> H H 1 N ; HYDROGEN BONDED TO NITROGEN
>>>>>>> H HO 1 O ; HYDROXYL HYDROGEN
>>>>>>> H HW 1 OW ; WATER HYDROGEN
>>>>>>> H HS 1 S ; HYDROGEN BONDED TO SULFUR
>>>>>>> H HC 1 C ; HYDROGEN BONDED TO CARBON
>>>>>>> S S 4 C 0.181 N 0.167 O 0.172 O 0.172
>>>>>>> F F 1 C
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> The Sulphur atoms have each 4 bonds but X2TOP wants them to have only
>>>>>>> 3. If I change the string in the N2T to 3 bonds, the topology is
>>>>>>> generated but S-C bond is absent.
>>>>>>>
>>>>>>> What can be the problem?
>>>>>>>
>>>>>>> Thanks.
>>>>>>> --
>>>>>>> Vitaly V. Chaban, Ph.D.
>>>>>>> http://www-rmn.univer.kharkov.ua/chaban.html
>>>>>>>
>>>>
>>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>>
>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
--
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
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