Comments (15)
JMorado
commented on May 27, 2024
Hi,
If you look at the "norfloxacin_sym.ff" produced after you set that you want to optimize all torsions that share the same symmetry with torsion_to_scan (norfloxacin.force_field.optimize_torsions_by_symmetry(torsion_to_scan)), you see the following:
PeriodicTorsionForce 2
0 0 1 2 36 1.00000000 0.00000000 8.36800000 0 0 0 T1
1 0 1 2 36 2.00000000 3.14159400 10.46000000 0 0 0 T0
2 0 1 24 50 1.00000000 0.00000000 8.36800000 0 0 0 T1
3 0 1 24 50 2.00000000 3.14159400 10.46000000 0 0 0 T0
4 2 1 24 50 2.00000000 3.14159400 10.46000000 0 0 0 T0
5 2 3 23 49 2.00000000 3.14159400 15.16700000 0 0 0 T3
6 2 3 4 37 2.00000000 3.14159400 15.16700000 0 0 0 T3
7 3 4 5 38 2.00000000 3.14159400 15.16700000 0 0 0 T3
8 4 3 2 36 2.00000000 3.14159400 1.88280000 0 0 0 T4
9 4 3 23 49 2.00000000 3.14159400 15.16700000 0 0 0 T3
10 4 5 6 39 2.00000000 3.14159400 15.16700000 0 0 0 T3
11 6 5 4 37 2.00000000 3.14159400 15.16700000 0 0 0 T3
12 6 7 23 49 2.00000000 3.14159400 15.16700000 0 0 0 T3
13 7 6 5 38 2.00000000 3.14159400 15.16700000 0 0 0 T3
14 7 8 9 40 2.00000000 3.14159400 16.73600000 0 0 0 T6
15 8 7 6 39 2.00000000 3.14159400 15.16700000 0 0 0 T3
16 8 7 23 49 2.00000000 3.14159400 15.16700000 0 0 0 T3
17 8 22 21 48 2.00000000 3.14159400 15.16700000 0 0 0 T3
18 8 9 10 41 2.00000000 3.14159400 7.11280000 0 0 0 T7
19 11 10 9 40 2.00000000 3.14159400 7.11280000 0 0 0 T7
20 11 22 21 48 2.00000000 3.14159400 15.16700000 0 0 0 T3
21 11 12 13 42 2.00000000 3.14159400 20.08320000 0 0 0 T9
22 12 11 10 41 2.00000000 3.14159400 1.25520000 0 0 0 T8
23 13 14 21 48 2.00000000 3.14159400 15.16700000 0 0 0 T3
24 14 15 20 47 2.00000000 3.14159400 15.16700000 0 0 0 T3
25 14 15 16 43 2.00000000 3.14159400 15.16700000 0 0 0 T3
26 15 14 13 42 2.00000000 3.14159400 15.16700000 0 0 0 T3
27 15 14 21 48 2.00000000 3.14159400 15.16700000 0 0 0 T3
28 15 20 19 46 2.00000000 3.14159400 15.16700000 0 0 0 T3
29 15 16 17 44 2.00000000 3.14159400 15.16700000 0 0 0 T3
30 16 15 20 47 2.00000000 3.14159400 15.16700000 0 0 0 T3
31 16 17 18 45 2.00000000 3.14159400 15.16700000 0 0 0 T3
32 17 18 19 46 2.00000000 3.14159400 15.16700000 0 0 0 T3
33 18 17 16 43 2.00000000 3.14159400 15.16700000 0 0 0 T3
34 18 19 20 47 2.00000000 3.14159400 15.16700000 0 0 0 T3
35 19 18 17 44 2.00000000 3.14159400 15.16700000 0 0 0 T3
36 20 15 16 43 2.00000000 3.14159400 15.16700000 0 0 0 T3
37 20 19 18 45 2.00000000 3.14159400 15.16700000 0 0 0 T3
38 21 14 13 42 2.00000000 3.14159400 15.16700000 0 0 0 T3
39 22 8 9 40 2.00000000 3.14159400 16.73600000 0 0 0 T6
40 22 11 10 41 2.00000000 3.14159400 1.25520000 0 0 0 T8
41 23 3 2 36 2.00000000 3.14159400 1.88280000 0 0 0 T4
42 23 3 4 37 2.00000000 3.14159400 15.16700000 0 0 0 T3
43 23 7 6 39 2.00000000 3.14159400 15.16700000 0 0 0 T3
44 24 1 2 36 2.00000000 3.14159400 10.46000000 0 0 0 T0
45 24 25 26 51 2.00000000 3.14159400 15.16700000 0 0 0 T3
46 25 34 33 53 2.00000000 3.14159400 15.16700000 0 0 0 T3
47 26 25 24 50 2.00000000 3.14159400 1.88280000 0 0 0 T4
48 26 27 32 52 2.00000000 3.14159400 15.16700000 0 0 0 T3
49 27 32 33 53 2.00000000 3.14159400 15.16700000 0 0 0 T3
50 28 27 26 51 2.00000000 3.14159400 15.16700000 0 0 0 T3
51 28 27 32 52 2.00000000 3.14159400 15.16700000 0 0 0 T3
52 32 27 26 51 2.00000000 3.14159400 15.16700000 0 0 0 T3
53 34 25 24 50 2.00000000 3.14159400 1.88280000 0 0 0 T4
54 34 25 26 51 2.00000000 3.14159400 15.16700000 0 0 0 T3
55 34 33 32 52 2.00000000 3.14159400 15.16700000 0 0 0 T3
56 35 34 33 53 2.00000000 3.14159400 15.16700000 0 0 0 T3
57 37 4 5 38 2.00000000 3.14159400 15.16700000 0 0 0 T3
58 38 5 6 39 2.00000000 3.14159400 15.16700000 0 0 0 T3
59 40 9 10 41 2.00000000 3.14159400 7.11280000 0 0 0 T7
60 43 16 17 44 2.00000000 3.14159400 15.16700000 0 0 0 T3
61 44 17 18 45 2.00000000 3.14159400 15.16700000 0 0 0 T3
62 45 18 19 46 2.00000000 3.14159400 15.16700000 0 0 0 T3
63 46 19 20 47 2.00000000 3.14159400 15.16700000 0 0 0 T3
64 52 32 33 53 2.00000000 3.14159400 15.16700000 0 0 0 T3
65 1 3 2 36 2.00000000 3.14159400 4.60240000 0 0 0 T13
66 3 5 4 37 2.00000000 3.14159400 4.60240000 0 0 0 T13
67 4 6 5 38 2.00000000 3.14159400 4.60240000 0 0 0 T13
68 5 7 6 39 2.00000000 3.14159400 4.60240000 0 0 0 T13
69 8 40 9 10 2.00000000 3.14159400 4.60240000 0 0 0 T13
70 11 9 10 41 2.00000000 3.14159400 4.60240000 0 0 0 T13
71 14 42 13 12 2.00000000 3.14159400 4.60240000 0 0 0 T13
72 17 15 16 43 2.00000000 3.14159400 4.60240000 0 0 0 T13
73 16 18 17 44 2.00000000 3.14159400 4.60240000 0 0 0 T13
74 17 19 18 45 2.00000000 3.14159400 4.60240000 0 0 0 T13
75 18 20 19 46 2.00000000 3.14159400 4.60240000 0 0 0 T13
76 19 15 20 47 2.00000000 3.14159400 4.60240000 0 0 0 T13
77 22 14 21 48 2.00000000 3.14159400 4.60240000 0 0 0 T13
78 3 7 23 49 2.00000000 3.14159400 4.60240000 0 0 0 T13
79 1 25 24 50 2.00000000 3.14159400 4.60240000 0 0 0 T13
80 25 27 26 51 2.00000000 3.14159400 4.60240000 0 0 0 T13
81 27 33 32 52 2.00000000 3.14159400 4.60240000 0 0 0 T13
82 32 34 33 53 2.00000000 3.14159400 4.60240000 0 0 0 T13
83 0 1 2 3 2.00000000 3.14159400 10.46000000 0 0 0 T0
84 0 1 24 25 2.00000000 3.14159400 10.46000000 0 0 0 T0
85 1 2 3 23 2.00000000 3.14159400 3.97480000 0 0 0 T2
86 1 2 3 4 2.00000000 3.14159400 3.97480000 0 0 0 T2
87 1 24 25 34 2.00000000 3.14159400 3.97480000 0 0 0 T2
88 1 24 25 26 2.00000000 3.14159400 3.97480000 0 0 0 T2
89 2 1 24 25 2.00000000 3.14159400 10.46000000 0 0 0 T0
90 2 3 23 7 2.00000000 3.14159400 15.16700000 0 0 0 T3
91 2 3 4 5 2.00000000 3.14159400 15.16700000 0 0 0 T3
92 3 2 1 24 2.00000000 3.14159400 10.46000000 0 0 0 T0
93 3 23 7 6 2.00000000 3.14159400 15.16700000 0 0 0 T3
94 3 23 7 8 2.00000000 3.14159400 15.16700000 0 0 0 T3
95 3 4 5 6 2.00000000 3.14159400 15.16700000 0 0 0 T3
96 4 3 23 7 2.00000000 3.14159400 15.16700000 0 0 0 T3
97 4 5 6 7 2.00000000 3.14159400 15.16700000 0 0 0 T3
98 5 4 3 23 2.00000000 3.14159400 15.16700000 0 0 0 T3
99 5 6 7 8 2.00000000 3.14159400 15.16700000 0 0 0 T3
100 5 6 7 23 2.00000000 3.14159400 15.16700000 0 0 0 T3
101 6 7 8 22 2.00000000 3.14159400 2.11292000 0 0 0 T5
102 6 7 8 9 2.00000000 3.14159400 2.11292000 0 0 0 T5
103 7 8 22 11 2.00000000 3.14159400 2.11292000 0 0 0 T5
104 7 8 22 21 2.00000000 3.14159400 2.11292000 0 0 0 T5
105 7 8 9 10 2.00000000 3.14159400 16.73600000 0 0 0 T6
106 8 22 11 10 2.00000000 3.14159400 15.16700000 0 0 0 T3
107 8 22 11 12 2.00000000 3.14159400 15.16700000 0 0 0 T3
108 8 22 21 14 2.00000000 3.14159400 15.16700000 0 0 0 T3
109 8 9 10 11 2.00000000 3.14159400 7.11280000 0 0 0 T7
110 9 8 7 23 2.00000000 3.14159400 2.11292000 0 0 0 T5
111 9 8 22 11 2.00000000 3.14159400 2.11292000 0 0 0 T5
112 9 8 22 21 2.00000000 3.14159400 2.11292000 0 0 0 T5
113 9 10 11 22 2.00000000 3.14159400 1.25520000 0 0 0 T8
114 9 10 11 12 2.00000000 3.14159400 1.25520000 0 0 0 T8
115 10 9 8 22 2.00000000 3.14159400 16.73600000 0 0 0 T6
116 10 11 22 21 2.00000000 3.14159400 15.16700000 0 0 0 T3
117 10 11 12 13 2.00000000 3.14159400 20.08320000 0 0 0 T9
118 11 22 21 14 2.00000000 3.14159400 15.16700000 0 0 0 T3
119 11 12 13 14 2.00000000 3.14159400 20.08320000 0 0 0 T9
120 12 11 22 21 2.00000000 3.14159400 15.16700000 0 0 0 T3
121 12 13 14 15 2.00000000 3.14159400 15.16700000 0 0 0 T3
122 12 13 14 21 2.00000000 3.14159400 15.16700000 0 0 0 T3
123 13 12 11 22 2.00000000 3.14159400 20.08320000 0 0 0 T9
124 13 14 15 20 2.00000000 3.14159400 3.32628000 0 0 0 T10
125 13 14 15 16 2.00000000 3.14159400 3.32628000 0 0 0 T10
126 13 14 21 22 2.00000000 3.14159400 15.16700000 0 0 0 T3
127 14 15 20 19 2.00000000 3.14159400 15.16700000 0 0 0 T3
128 14 15 16 17 2.00000000 3.14159400 15.16700000 0 0 0 T3
129 15 14 21 22 2.00000000 3.14159400 15.16700000 0 0 0 T3
130 15 20 19 18 2.00000000 3.14159400 15.16700000 0 0 0 T3
131 15 16 17 18 2.00000000 3.14159400 15.16700000 0 0 0 T3
132 16 15 14 21 2.00000000 3.14159400 3.32628000 0 0 0 T10
133 16 15 20 19 2.00000000 3.14159400 15.16700000 0 0 0 T3
134 16 17 18 19 2.00000000 3.14159400 15.16700000 0 0 0 T3
135 17 16 15 20 2.00000000 3.14159400 15.16700000 0 0 0 T3
136 17 18 19 20 2.00000000 3.14159400 15.16700000 0 0 0 T3
137 20 15 14 21 2.00000000 3.14159400 3.32628000 0 0 0 T10
138 22 8 7 23 2.00000000 3.14159400 2.11292000 0 0 0 T5
139 24 25 34 33 2.00000000 3.14159400 15.16700000 0 0 0 T3
140 24 25 34 35 2.00000000 3.14159400 15.16700000 0 0 0 T3
141 24 25 26 27 2.00000000 3.14159400 15.16700000 0 0 0 T3
142 25 34 33 32 2.00000000 3.14159400 15.16700000 0 0 0 T3
143 25 26 27 28 2.00000000 3.14159400 15.16700000 0 0 0 T3
144 25 26 27 32 2.00000000 3.14159400 15.16700000 0 0 0 T3
145 26 25 34 33 2.00000000 3.14159400 15.16700000 0 0 0 T3
146 26 25 34 35 2.00000000 3.14159400 15.16700000 0 0 0 T3
147 26 27 28 29 2.00000000 0.00000000 0.00000000 0 0 0 T11
148 26 27 28 30 2.00000000 0.00000000 0.00000000 0 0 0 T11
149 26 27 28 31 2.00000000 0.00000000 0.00000000 0 0 0 T11
150 26 27 32 33 2.00000000 3.14159400 15.16700000 0 0 0 T3
151 27 26 25 34 2.00000000 3.14159400 15.16700000 0 0 0 T3
152 27 32 33 34 2.00000000 3.14159400 15.16700000 0 0 0 T3
153 28 27 32 33 2.00000000 3.14159400 15.16700000 0 0 0 T3
154 29 28 27 32 2.00000000 0.00000000 0.00000000 0 0 0 T11
155 30 28 27 32 2.00000000 0.00000000 0.00000000 0 0 0 T11
156 31 28 27 32 2.00000000 0.00000000 0.00000000 0 0 0 T11
157 32 33 34 35 2.00000000 3.14159400 15.16700000 0 0 0 T3
158 0 1 24 2 2.00000000 3.14159400 43.93200000 0 0 0 T12
159 4 23 3 2 2.00000000 3.14159400 4.60240000 0 0 0 T13
160 6 23 7 8 2.00000000 3.14159400 4.60240000 0 0 0 T13
161 7 22 8 9 2.00000000 3.14159400 4.60240000 0 0 0 T13
162 22 10 11 12 2.00000000 3.14159400 4.60240000 0 0 0 T13
163 13 21 14 15 2.00000000 3.14159400 4.60240000 0 0 0 T13
164 16 20 15 14 2.00000000 3.14159400 4.60240000 0 0 0 T13
165 11 21 22 8 2.00000000 3.14159400 4.60240000 0 0 0 T13
166 26 34 25 24 2.00000000 3.14159400 4.60240000 0 0 0 T13
167 26 32 27 28 2.00000000 3.14159400 4.60240000 0 0 0 T13
168 25 33 34 35 2.00000000 3.14159400 4.60240000 0 0 0 T13
Clearly, there is no torsion in the topology that is formed by the quartet of atoms [27, 28, 29, 30]. Therefore, ParaMol is not able to identify its symmetry, and then the optimization will try to fit 0 parameters, hence the error.
Try to choose a torsion that is listed, even if that is not the one you've scanned (they should be related, though...).
I will add some assertions and more verbose to try to minimize these errors.
Best,
João
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kexul
commented on May 27, 2024
Hi, @JMorado , thanks for the quick reply!
The prmtop and inpcrd file was generated by acpype( which use ambertools and gaff forcefield), and the [27, 28, 29, 30] was a c-c-c-f dihedral, whose parameters was zero in the generated files.
The purpose I use Paramol was to fill up the missing parameters. Is this the correct usage of paramol?
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JMorado
commented on May 27, 2024
Yes, you can optimize any parameters that are contained in the prmtop file, but it seems that the 27-28-29-30 is not there.
The reason for that may be that that specific dihedral has a force constant of 0 and, therefore, it is not included in the prmtop file because it does not contribute to the energy. What I usually do in these situations is to change the force constant in the frcmod file to, for example, 0.001. Leap will then include it in the prmtop file.
The same argument works for two different dihedrals with the same parameters. Say you have the following lines in the frcmod file:
ca-ca-ca-c3 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-f 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
To save memory, LEAP assumes that these share the same symmetry. If you want to optimize them independently you'll have to change the frcmod to something like:
ca-ca-ca-c3 1 3.6251 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-f 1 3.6250 180.000 2.0 SCEE=1.2 SCNB=2.0
Note the small change in force constant. LEAP then assumes that these are two different dihedral types, and they will appear as so in the prmtop file.
Hope this helps.
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JMorado
commented on May 27, 2024
Actually, I think the dihedrals with force constant 0 were included in the prmtop file. If you look at these lines in the .ff file:
147 26 27 28 29 2.00000000 0.00000000 0.00000000 0 0 0 T11
148 26 27 28 30 2.00000000 0.00000000 0.00000000 0 0 0 T11
149 26 27 28 31 2.00000000 0.00000000 0.00000000 0 0 0 T11
These are dihedrals with a force constant of 0. The 26-27-28-30 and 26-27-28-31 are ca-ca-ca-f whereas 26-27-28-29 is ca-ca-ca-c3. They share the same symmetry (T11), but you may want to break it with the procedure I explained in the previous message.
You can then use the dihedral scan you generated to optimize the c-c-c-f dihedral parameters of the 26-27-28-30 and 26-27-28-31 dihedrals. Set them for optimization using:
norfloxacin.force_field.optimize_torsions_by_symmetry([[26,27,38,30]])
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kexul
commented on May 27, 2024
Thanks so much for your help! I've tried 26-27-28-30, no error occurred. I'll try modify the frcmod as you said and report it back to you if that helps.
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JMorado
commented on May 27, 2024
Let me know if you have any further questions.
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kexul
commented on May 27, 2024
Hi @JMorado , I've tried modify the frcmod file, add a small force constant, and use tleap to generate an new prmtop file, but the dihedral ca-ca-c3-f was still not included in the generated norfloxacin_sym.ff file.
Here is the files I've used:
new.zip
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kexul
commented on May 27, 2024
Besides, I used atom index from 1 as in pdb file. In the .ff file, the atom index was started from 0, should I set torsion_to_scan parameter using atom index started from zero?
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JMorado
commented on May 27, 2024
Hi @kexul .
I think the ca-ca-c3-f dihedrals are already included. From what I can see, these are the dihedrals you are interested in (numbering does not match with the figure above):
114 20 21 22 23 2.00000000 3.14159400 0.00418400 0 0 0 T10
115 20 21 22 24 2.00000000 3.14159400 0.00418400 0 0 0 T10
116 20 21 22 25 2.00000000 3.14159400 0.00418400 0 0 0 T10
117 23 22 21 26 2.00000000 3.14159400 0.00418400 0 0 0 T10
118 24 22 21 26 2.00000000 3.14159400 0.00418400 0 0 0 T10
119 25 22 21 26 2.00000000 3.14159400 0.00418400 0 0 0 T10
And actually, I have just re-checked, and they were also already included in the RB2345_AC.prmtop (see T11 symmetries):
147 26 27 28 29 2.00000000 0.00000000 0.00000000 0 0 0 T11
148 26 27 28 30 2.00000000 0.00000000 0.00000000 0 0 0 T11
149 26 27 28 31 2.00000000 0.00000000 0.00000000 0 0 0 T11
150 26 27 32 33 2.00000000 3.14159400 15.16700000 0 0 0 T3
151 27 26 25 34 2.00000000 3.14159400 15.16700000 0 0 0 T3
152 27 32 33 34 2.00000000 3.14159400 15.16700000 0 0 0 T3
153 28 27 32 33 2.00000000 3.14159400 15.16700000 0 0 0 T3
154 29 28 27 32 2.00000000 0.00000000 0.00000000 0 0 0 T11
155 30 28 27 32 2.00000000 0.00000000 0.00000000 0 0 0 T11
156 31 28 27 32 2.00000000 0.00000000 0.00000000 0 0 0 T11
The numbering in the figure was what led me to think that the T11 dihedrals belonged to different dihedral types. They actually do not! So you are good to go and scan one of those T11 dihedral. Just remember that ParaMol starts atom indexing from 0.
Furthermore, in the new files you've sent me, it wasn't actually necessary to break the symmetry of the ca-ca-c3-f and f -c3-ca-ca because they already have different parameters and, therefore, are considered to be different dihedral types. That only applies to dihedral types like these:
ca-ca-cd-cc 1 0.505 180.000 2.000 same as c2-ce-ca-ca, penalty score=229.0
ca-ca-cd-ca 1 0.505 180.000 2.000 same as c2-ce-ca-ca, penalty score=229.0
So, if you, e.g., wanted to independently optimize the parameters of the ca-ca-cd-cc and ca-ca-cd-ca, you'd have to break their symmetry.
Best,
João
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kexul
commented on May 27, 2024
Wow, thanks so much for your continued help! The new atom index worked like a charm.
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kexul
commented on May 27, 2024
Hi @JMorado , the parametrization terminated successfully! But when I check the frcmod file generated, the value of ca-ca-c3-f seems very different from other values(the phase was not 180, the force constant was very large).
ca-ca-ca-c3 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-f 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-c3-f 1 -11.26833001 13.696 2.0 SCEE=1.2 SCNB=2.0
nv-ca-ca-ha 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-ha 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
hn-nv-ca-ca 1 1.05000000 180.000 2.0 SCEE=1.2 SCNB=2.0
Is this a good result?
Here is part of my output when running paramol:
ata of system norfloxacin was written to file norfloxacin_scan.nc
!=================================================================================!
! PARAMETRIZATION !
!=================================================================================!
!=================================================================================!
! Scaling Constants !
! Term type Value !
!---------------------------------------------------------------------------------!
! torsion_phase 3.14159265 !
! torsion_k 16.73600000 !
!=================================================================================!
!=================================================================================!
! Prior Widths !
! Term type Value !
!---------------------------------------------------------------------------------!
! torsion_phase 3.14159265 !
! torsion_k 16.73600000 !
!=================================================================================!
!=================================================================================!
! Objective Function Analysis !
! PROPERTY Value x Weight = Contribution !
!---------------------------------------------------------------------------------!
! ENERGY 63.34887833 1.00000000 63.34887833 !
! REGULARIZATION 0.00000000 1.00000000 0.00000000 !
! TOTAL 63.34887833 !
!---------------------------------------------------------------------------------!
! Function Evaluations: 0 Time (s): 0.002 !
!=================================================================================!
Using 4 structures in the optimization.
Number of parameters to be optimized: 2.
ParaMol will perform unconstrained optimization.
!=================================================================================!
! STARTING SCIPY OPTIMIZER !
!=================================================================================!
/data/miniconda3/envs/uii/lib/python3.7/site-packages/scipy/optimize/_minimize.py:525: RuntimeWarning: Method SLSQP does not use Hessian information (hess).
RuntimeWarning)
/data/miniconda3/envs/uii/lib/python3.7/site-packages/ParaMol/Optimizers/scipy_optimizers.py:67: OptimizeWarning: Unknown solver options: verbosity
optimization = minimize(fun=f, x0=parameters, **self.__dict__)
NIT FC OBJFUN GNORM
1 4 6.520047E+03 3.461633E+01
2 8 1.334427E+05 8.956616E+01
3 14 1.373651E+01 1.646591E+01
4 17 1.369743E+01 8.671029E+00
5 20 1.369652E+01 1.305434E+00
6 23 1.369652E+01 4.902052E-03
Optimization terminated successfully (Exit mode 0)
Current function value: 13.696521568505162
Iterations: 6
Function evaluations: 32
Gradient evaluations: 6
!=================================================================================!
! SCIPY OPTIMIZER TERMINATED SUCCESSFULLY! :) !
!=================================================================================!
!=================================================================================!
! Objective Function Analysis !
! PROPERTY Value x Weight = Contribution !
!---------------------------------------------------------------------------------!
! ENERGY 5.75477795 1.00000000 5.75477795 !
! REGULARIZATION 7.94174362 1.00000000 7.94174362 !
! TOTAL 13.69652157 !
!---------------------------------------------------------------------------------!
! Function Evaluations: 32 Time (s): 0.002 !
!=================================================================================!
!=================================================================================!
! PARAMETRIZATION TERMINATED SUCCESSFULLY :) !
!=================================================================================!
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JMorado
commented on May 27, 2024
Parameters may be very dependent on the system, but I would say that those are really large values...
If these are the scan_settings = [[-180.0, 180.0, 90.0]] you are using, then you should definitely decrease the spacing to something to something like [[-180.0, 180.0, 10.0]]
Also, I recommend using Boltzmann or Non-Boltzmann weighting to weight the conformations in the optimization:
paramol_settings.objective_function["weighting_method"] = "boltzmann"
paramol_settings.objective_function["weighting_temperature"] = 300.0*unit.kelvin
DFTB works fine for some initial tests, but the final results should be computed using higher levels of theory.
You can plot the results also to see how they look like. The scan QM energies are stored in norfloxacin.ref_energies and the MM energies before and after the optimization can be computed calling the method norfloxacin.get_energies_ensemble()
Off the top of my head, these are some of the aspects that may help you improve the parameterizations...
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kexul
commented on May 27, 2024
Thanks @JMorado . I've tried decrease the spacing and use boltzmann, now it becomes even larger...
ca-ca-ca-c3 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-f 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-c3-f 1 -14.32510008 -31.655 2.0 SCEE=1.2 SCNB=2.0
nv-ca-ca-ha 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-ha 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
hn-nv-ca-ca 1 1.05000000 180.000 2.0 SCEE=1.2 SCNB=2.0
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JMorado
commented on May 27, 2024
I advise you to look at the plots of the scans. It's impossible to understand if that is a good or bad result without that.
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kexul
commented on May 27, 2024
I advise you to look at the plots of the scans. It's impossible to understand if that is a good or bad result without that.
Thanks, I'll try that.
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