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 21:59:04 CET 2010
Vitaly V. Chaban wrote:
> 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
>
Is this to be used with the original .pdb file you posted? I ran it through and
it failed with a very important (I think) error:
"There are 0 name to type translations"
As before, the format of your .n2t file is incorrect. Build a suitable file and
try again.
-Justin
>
> 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
>>
>> ========================================
>>
>
>
>
--
========================================
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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