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 20:13:01 CET 2010
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.
> 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
========================================
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