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 20:06:42 CET 2010
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?
In my case, maybe it considers that 0.18 nm is too much for two atoms
to be connected?
---------- 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
>>>
>>
--
Vitaly V. Chaban, Ph.D.
http://www-rmn.univer.kharkov.ua/chaban.html
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