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 <vvcha...@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: jalem...@vt.edu, gmx-users@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 <jalem...@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 <vvcha...@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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