Fwd: [gmx-users] Re: x2top and bonds. No forcefield type for atom S (2) with 3 bonds
Justin A. Lemkul
jalemkul at vt.edu
Fri Feb 5 21:13:27 CET 2010
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
========================================
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