Specifying bonds only for asymmetric unit cell parts

GULP
1

I see even the most simple force field (Dreading) need bond order specification.

But e.g. gaff2 does not work with bond order at all so single autobond created are OK (because gaff2 identify forces base don atom types) … Correct ?

Question:

Can I specify only the bonds in the asymmetric unit cell part and let GULP generate the rest of the cell by symmetrically related molecules with identical bond types ?
Under the assumption there are no cross-symmetry, inter cell bonds ?
I am afraid this is impossible because GULP can not utilize the correct information about bonding in the asymmetric unit to fill the whole cell … Correct ?

Otherwise for automatic generation in gulp, I must give each atom a specific label and specify the bond type to the other labeled atom … And create a huge force-field translation table translating all labels to FF types … Correct ?

2

Dreiding (note spelling as dreading is an amusing way of describing it, assuming you really don’t like this force field!) isn’t the simplest force field as a Lennard-Jones plus Coulomb be simpler. If you specifically say “molecular force field” then you come closer.
If you specify the right atom types in the asymmetric unit then you can set all the bonds to the right type with the “bondtype” option and automatic bonding generation.

3

Dear Mr. Gale

Thank you for your explanation. The miss spell of the Dreiding was non-intentional. It is a nice force field suitable for different MM engines comparison.

I can confirm that with GULP 6.3.1. I am able to get 100% identical results for a structure entered in space group P212121 with bonds defined by sequence like in my case:

bondtype C1 C1 resonant
bondtype N1 C1 resonant
bondtype C3 O2 double
bondtype C1 C3 single exocyclic

and Materials Studio GULP run in space group P1 with all bonds pre-generated by Materials Studio.
Dreiding ff, Gasteiger charges (Antechamber versus MS engine), automatic atom types assignment (Antechamber versus MS engine with manual correction for the X_R non standard behavior)
The 100% correspondence was confirmed by CIF analysis in Mercury (Crystal Packing Similarity) …
I can now work on 100% automatization of this process (for Dreiding, UFF, gaff ,gaff2).

If you want eventually put such test in your examples, the .gin file follows:

opti conse qok nomod pres conp
ftol 1e-005
gtol 0.0001
xtol 1e-005
maxcyc 1000

title
GULP calculation from checkCIF-DFT for: Nicergoline P212121
end

cell
11.507 13.219 14.753 90 90 90 1 1 1 1 1 1

fractional
Br1 core  -0.02048 0.82131 0.22983 -0.049132 1.000000 0.0 1 1 1
O1 core  0.3108 0.4338 0.2257 -0.311745 1.000000 0.0 1 1 1
O2 core  0.354 0.5771 0.3 -0.260634 1.000000 0.0 1 1 1
O1 core  0.2821 0.1318 0.4464 -0.371847 1.000000 0.0 1 1 1
N1 core  0.4797 -0.2148 0.465 -0.309542 1.000000 0.0 1 1 1
N2 core  0.2553 0.1204 0.2551 -0.299495 1.000000 0.0 1 1 1
N1 core  0.0301 0.5517 0.0974 -0.262711 1.000000 0.0 1 1 1
C1 core  0.3829 -0.2029 0.4112 -0.000592 1.000000 0.0 1 1 1
C1 core  0.363 -0.1029 0.3948 -0.022721 1.000000 0.0 1 1 1
C2 core  0.2788 -0.0436 0.3372 -0.007096 1.000000 0.0 1 1 1
C2 core  0.3376 0.057 0.3073 0.046677 1.000000 0.0 1 1 1
C2 core  0.3125 0.214 0.2245 0.003443 1.000000 0.0 1 1 1
C2 core  0.3478 0.2781 0.3052 -0.001256 1.000000 0.0 1 1 1
C2 core  0.4351 0.2187 0.362 -0.011732 1.000000 0.0 1 1 1
C2 core  0.3835 0.1174 0.3908 0.109489 1.000000 0.0 1 1 1
C1 core  0.4737 0.053 0.4404 -0.005211 1.000000 0.0 1 1 1
C1 core  0.5708 0.0854 0.4862 -0.055335 1.000000 0.0 1 1 1
C1 core  0.6432 0.0156 0.5306 -0.059971 1.000000 0.0 1 1 1
C1 core  0.6228 -0.0872 0.53 -0.039973 1.000000 0.0 1 1 1
C1 core  0.5234 -0.1202 0.4843 0.040201 1.000000 0.0 1 1 1
C1 core  0.4516 -0.0501 0.4397 0.006611 1.000000 0.0 1 1 1
C2 core  0.5227 -0.3106 0.4999 0.004683 1.000000 0.0 1 1 1
C2 core  0.2077 0.0674 0.1745 -0.012937 1.000000 0.0 1 1 1
C2 core  0.4007 0.3774 0.2755 0.060828 1.000000 0.0 1 1 1
C3 core  0.2943 0.5299 0.2476 0.294249 1.000000 0.0 1 1 1
C1 core  0.1884 0.5713 0.2021 0.066435 1.000000 0.0 1 1 1
C1 core  0.1295 0.5188 0.1349 0.040196 1.000000 0.0 1 1 1
C1 core  -0.0128 0.6386 0.1276 0.041014 1.000000 0.0 1 1 1
C1 core  0.0435 0.6959 0.1927 0.036643 1.000000 0.0 1 1 1
C1 core  0.1461 0.6628 0.2304 -0.031441 1.000000 0.0 1 1 1
C2 core  0.2984 0.1795 0.5315 0.036759 1.000000 0.0 1 1 1
H1 core  0.3339 -0.2595 0.3874 0.079497 1.000000 0.0 1 1 1
H1 core  0.2069 -0.0285 0.3728 0.03341 1.000000 0.0 1 1 1
H1 core  0.258 -0.0842 0.2823 0.03341 1.000000 0.0 1 1 1
H1 core  0.4028 0.0411 0.2648 0.050459 1.000000 0.0 1 1 1
H1 core  0.3832 0.1961 0.1885 0.043442 1.000000 0.0 1 1 1
H1 core  0.2574 0.2531 0.1855 0.043442 1.000000 0.0 1 1 1
H1 core  0.2767 0.2951 0.341 0.034104 1.000000 0.0 1 1 1
H1 core  0.4559 0.2588 0.4171 0.030457 1.000000 0.0 1 1 1
H1 core  0.5065 0.2062 0.3251 0.030457 1.000000 0.0 1 1 1
H1 core  0.5902 0.1592 0.4878 0.0627 1.000000 0.0 1 1 1
H1 core  0.7126 0.0415 0.5642 0.062355 1.000000 0.0 1 1 1
H1 core  0.6765 -0.1357 0.5609 0.064291 1.000000 0.0 1 1 1
H1 core  0.594 -0.2985 0.537 0.043611 1.000000 0.0 1 1 1
H1 core  0.4615 -0.3428 0.5385 0.043611 1.000000 0.0 1 1 1
H1 core  0.5419 -0.3564 0.4481 0.043611 1.000000 0.0 1 1 1
H1 core  0.1527 0.1132 0.1417 0.039422 1.000000 0.0 1 1 1
H1 core  0.2727 0.0479 0.1331 0.039422 1.000000 0.0 1 1 1
H1 core  0.1654 0.0053 0.1947 0.039422 1.000000 0.0 1 1 1
H1 core  0.4268 0.4169 0.3297 0.057703 1.000000 0.0 1 1 1
H1 core  0.4687 0.3644 0.2349 0.057703 1.000000 0.0 1 1 1
H1 core  0.1628 0.4532 0.1134 0.084871 1.000000 0.0 1 1 1
H1 core  -0.0882 0.6637 0.1024 0.085212 1.000000 0.0 1 1 1
H1 core  0.1883 0.7042 0.2766 0.064441 1.000000 0.0 1 1 1
H1 core  0.2219 0.1851 0.5633 0.053031 1.000000 0.0 1 1 1
H1 core  0.3531 0.1385 0.5692 0.053031 1.000000 0.0 1 1 1
H1 core  0.3315 0.2486 0.5219 0.053031 1.000000 0.0 1 1 1

Species
Br1 core Br
O1 core O_3
O2 core O_2
N1 core N_R
N2 core N_3
C1 core C_R
C2 core C_3
C3 core C_2
H1 core H_

bondtype C1 C1 resonant
bondtype N1 C1 resonant
bondtype C3 O2 double
bondtype C1 C3 single exocyclic

spacegroup
P 21 21 21

library dreiding

output cif nicer_P212121_Z4-out
4

After some experiments I see following situation can not be solved:
When atom of given type create 2 or more different sort of bonds. This can happen normaly - bond type can differ on bonded atoms surrounding.
And becouse GULP does not accept asociation of multiple types to the same Specie, I can not give for atoms bond types individualy.
Explanation:
Let C1 be SP2 carbon, Dreiding C_2
So some C1 C1 can be single bond, some can be double bond …
I can mark tehem e.g. C1 and C2 and tell:
bondtype C1 C1 single
bondtype C2 C1 double
But I can not than use:
Species
C1 core C_2
C2 core C_2
Any solution ?

5

You can use “dump connect” with a single point calculation to write out the bonds & then set the types according to what you want for each individual bond.