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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