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 21:07:51 CET 2010
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...
>> 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
>
> ========================================
>
--
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
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