[gmx-users] 100-quartz force field for GROMACS using CGenFF
Ivan Gladich
igladich at sissa.it
Sun Mar 5 12:56:26 CET 2017
Dear all,
I would like to simulate an alpha-quartz (100) hydroxylated/hydrogenated
interface using GROAMCS.
Force field parameters and structure are available in CHARMM
(http://mackerell.umaryland.edu/charmm_ff.shtml) and reported in the
supplemental material of Lopes, P.E.M., Murashov, V., Tazi, M., Demchuk,
E. and MacKerell, Jr., A.D. "Development of an Empirical Force Field for
Silica. Application to the Quartz-Water Interface," Journal of Physcial
Chemistry B 110: 2782-2792, 2006.
Since I am not familiar with CHARMM force field (and crystal simulations
as well), my plan was to create the FF in CHARMM and then convert it to
GMX format. I copied the quartz (100) structure reported in the paper
above, converting it in .mol2 format, adding PBC information (see mol2
attached below).
Then I tried using CHARMM General Force Field (CGenFF) program
(https://cgenff.paramchem.org) uploading my .mol2 file. If I understand
correctly, the quartz parameters reported in the paper above should be
present in CGenFF program. However, I am getting error of the type:
"Now processing molecule Q100 ... attype warning: element not
supported;skipped molecule."
Since I read from this mailing list that some of you currently use
CGenFF, I would like to ask whether some of you have some advise on
how to get this force field for this structure running in GROAMCS, using
CGenFF or any other alternative way.
Thank you very much for any possible help or hint.
Ivan
@<TRIPOS>MOLECULE
Q100
43 40 3
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 Si 0.1700 1.0500 13.0600 Si 1 Si
0.0000
2 Si1 0.1700 3.5000 17.3100 Si 1 Si
0.0000
3 Si2 0.1700 1.0500 21.5600 Si 1 Si
0.0000
4 Si3 0.1700 3.5000 25.8100 Si 1 Si
0.0000
5 O 0.8000 1.5400 11.6500 O 2 O
0.0000
6 O1 0.8000 3.9900 15.9000 O 2 O
0.0000
7 O2 0.8000 1.5400 20.1500 O 2 O
0.0000
8 O3 0.8000 3.9900 24.4100 O 2 O
0.0000
9 O4 4.4000 2.0500 13.5000 O 2 O
0.0000
10 O5 4.4000 4.5000 17.7500 O 2 O
0.0000
11 O6 4.4000 2.0500 22.0100 O 2 O
0.0000
12 O7 4.4000 4.5000 26.2600 O 2 O
0.0000
13 O8 4.9400 4.5000 12.7700 O 2 O
0.0000
14 O9 4.9400 2.0500 17.0300 O 2 O
0.0000
15 O10 4.9400 4.5000 21.2800 O 2 O
0.0000
16 O11 4.9400 2.0500 25.5300 O 2 O
0.0000
17 O12 1.3400 0.9400 14.1400 O 2 O
0.0000
18 O13 1.3400 3.3900 18.3900 O 2 O
0.0000
19 O14 1.3400 0.9400 22.6400 O 2 O
0.0000
20 O15 1.3400 3.3900 26.9000 O 2 O
0.0000
21 Si4 1.9700 2.4200 11.0100 Si 1 Si
0.0000
22 Si5 1.9700 -0.0400 15.2600 Si 1 Si
0.0000
23 Si6 1.9700 2.4200 19.5200 Si 1 Si
0.0000
24 Si7 1.9700 -0.0400 23.7700 Si 1 Si
0.0000
25 Si8 1.9700 2.4200 28.0200 Si 1 Si
0.0000
26 Si9 3.7700 3.5000 13.2200 Si 1 Si
0.0000
27 Si10 3.7700 1.0500 17.4700 Si 1 Si
0.0000
28 Si11 3.7700 3.5000 21.7200 Si 1 Si
0.0000
29 Si12 3.7700 1.0500 25.9800 Si 1 Si
0.0000
30 O16 2.6000 3.3900 12.1400 O 2 O
0.0000
31 O17 2.6000 0.9400 16.3900 O 2 O
0.0000
32 O18 2.6000 3.3900 20.6400 O 2 O
0.0000
33 O19 2.6000 0.9400 24.8900 O 2 O
0.0000
34 O20 3.1400 3.9900 14.6200 O 2 O
0.0000
35 O21 3.1400 1.5400 18.8800 O 2 O
0.0000
36 O22 3.1400 3.9900 23.1300 O 2 O
0.0000
37 O23 3.1400 1.5400 27.3800 O 2 O
0.0000
38 H 1.3400 3.3900 9.8900 H 3 H
0.0000
39 H1 3.1400 1.5400 10.3700 H 3 H
0.0000
40 O24 0.8000 1.5400 28.6600 O 2 O
0.0000
41 O25 2.6000 3.3900 29.1400 O 2 O
0.0000
42 H2 0.8000 1.5400 29.7600 H 3 H
0.0000
43 H3 2.6000 3.3900 30.2400 H 3 H
0.0000
@<TRIPOS>BOND
1 1 5 1
2 1 17 1
3 2 6 1
4 2 18 1
5 3 7 1
6 3 19 1
7 4 8 1
8 4 20 1
9 5 21 1
10 7 23 1
11 9 26 1
12 11 28 1
13 13 26 1
14 14 27 1
15 15 28 1
16 16 29 1
17 17 22 1
18 18 23 1
19 19 24 1
20 20 25 1
21 21 30 1
22 21 38 1
23 21 39 1
24 22 31 1
25 23 32 1
26 23 35 1
27 24 33 1
28 25 37 1
29 25 40 1
30 25 41 1
31 26 30 1
32 26 34 1
33 27 31 1
34 27 35 1
35 28 32 1
36 28 36 1
37 29 33 1
38 29 37 1
39 40 42 1
40 41 43 1
@<TRIPOS>SUBSTRUCTURE
1 Si 1 GROUP 0 **** 0 ROOT
2 O 5 GROUP 0 **** 0 ROOT
3 H 38 GROUP 0 **** 0 ROOT
@<TRIPOS>FF_PBC
v1.0 1 0.0 0.0 0.0 4.914 4.914 40.000 none
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