New atoms & torsional constraints

General Discussion
1

Here is more information:

Its Windows XP, Avogadro 1.01. Not sure if the list allows attachments so I have
also attached the PDB as text below.

I am trying to freeze atom ID numbers: 18-54-17-55
54, 55 are the newly added atoms.
Thanks again,
Prashanth
PDB file follows:

COMPND pgs_ebuild.pdb
AUTHOR GENERATED BY OPEN BABEL 2.2.3
HETATM 1 C LIG 1 5.042 -2.355 -0.634 1.00 0.00 C
HETATM 2 H LIG 1 5.354 -2.406 -1.723 1.00 0.00 H
HETATM 3 C LIG 1 5.351 -0.945 -0.061 1.00 0.00 C
HETATM 4 O LIG 1 5.321 -0.739 1.179 1.00 0.00 O
HETATM 5 N LIG 1 5.538 0.108 -0.923 1.00 0.00 N
HETATM 6 C LIG 1 5.939 -0.040 -2.320 1.00 0.00 C
HETATM 7 H LIG 1 6.695 -0.868 -2.423 1.00 0.00 H
HETATM 8 H LIG 1 5.033 -0.305 -2.934 1.00 0.00 H
HETATM 9 C LIG 1 6.556 1.297 -2.765 1.00 0.00 C
HETATM 10 H LIG 1 7.553 1.127 -3.242 1.00 0.00 H
HETATM 11 H LIG 1 5.895 1.795 -3.518 1.00 0.00 H
HETATM 12 C LIG 1 6.684 2.149 -1.506 1.00 0.00 C
HETATM 13 H LIG 1 6.366 3.203 -1.687 1.00 0.00 H
HETATM 14 H LIG 1 7.743 2.167 -1.146 1.00 0.00 H
HETATM 15 C LIG 1 5.796 1.459 -0.446 1.00 0.00 C
HETATM 16 H LIG 1 6.306 1.429 0.560 1.00 0.00 H
HETATM 17 C LIG 1 4.494 2.271 -0.239 1.00 0.00 C
HETATM 18 H LIG 1 3.841 1.778 -2.121 1.00 0.00 H
HETATM 19 C LIG 1 2.723 3.442 -1.526 1.00 0.00 C
HETATM 20 H LIG 1 3.117 4.382 -1.030 1.00 0.00 H
HETATM 21 C LIG 1 2.430 3.747 -3.017 1.00 0.00 C
HETATM 22 H LIG 1 2.031 2.809 -3.500 1.00 0.00 H
HETATM 23 C LIG 1 1.390 4.839 -3.155 1.00 0.00 C
HETATM 24 H LIG 1 1.358 5.196 -4.214 1.00 0.00 H
HETATM 25 H LIG 1 1.637 5.712 -2.504 1.00 0.00 H
HETATM 26 H LIG 1 0.372 4.460 -2.897 1.00 0.00 H
HETATM 27 C LIG 1 3.702 4.162 -3.732 1.00 0.00 C
HETATM 28 H LIG 1 4.433 3.320 -3.790 1.00 0.00 H
HETATM 29 H LIG 1 4.187 5.020 -3.206 1.00 0.00 H
HETATM 30 H LIG 1 3.463 4.478 -4.777 1.00 0.00 H
HETATM 31 C LIG 1 1.395 3.046 -0.827 1.00 0.00 C
HETATM 32 O LIG 1 1.007 1.862 -0.745 1.00 0.00 O
HETATM 33 N LIG 1 0.641 4.064 -0.272 1.00 0.00 N
HETATM 34 H LIG 1 0.916 5.008 -0.407 1.00 0.00 H
HETATM 35 C LIG 1 -0.510 3.813 0.553 1.00 0.00 C
HETATM 36 H LIG 1 -0.348 2.823 1.101 1.00 0.00 H
HETATM 37 C LIG 1 -0.721 4.869 1.647 1.00 0.00 C
HETATM 38 H LIG 1 0.195 4.892 2.299 1.00 0.00 H
HETATM 39 H LIG 1 -1.558 4.479 2.289 1.00 0.00 H
HETATM 40 C LIG 1 -1.006 6.264 1.131 1.00 0.00 C
HETATM 41 H LIG 1 -0.094 6.911 1.250 1.00 0.00 H
HETATM 42 H LIG 1 -1.252 6.235 0.034 1.00 0.00 H
HETATM 43 C LIG 1 -2.133 6.952 1.893 1.00 0.00 C
HETATM 44 H LIG 1 -1.971 6.848 3.005 1.00 0.00 H
HETATM 45 H LIG 1 -2.158 8.049 1.630 1.00 0.00 H
HETATM 46 N LIG 1 -3.471 6.380 1.573 1.00 0.00 N
HETATM 47 H LIG 1 -3.469 5.364 1.766 1.00 0.00 H
HETATM 48 H LIG 1 -4.204 6.841 2.113 1.00 0.00 H
HETATM 49 H LIG 1 -3.661 6.475 0.566 1.00 0.00 H
HETATM 50 C LIG 1 -1.823 3.612 -0.253 1.00 0.00 C
HETATM 51 O LIG 1 -2.832 4.333 -0.038 1.00 0.00 O
HETATM 52 N LIG 1 -1.838 2.612 -1.180 1.00 0.00 N
HETATM 53 H LIG 1 -1.042 2.008 -1.266 1.00 0.00 H
HETATM 54 N LIG 1 3.256 2.054 -1.005 1.00 0.00 N
HETATM 55 O LIG 1 4.181 2.231 0.708 1.00 0.00 O
CONECT 1 2 3
CONECT 2 1
CONECT 3 1 5 4 4
CONECT 4 3 3
CONECT 5 3 6 15
CONECT 6 5 8 9 7
CONECT 7 6
CONECT 8 6
CONECT 9 6 11 10 12
CONECT 10 9
CONECT 11 9
CONECT 12 9 13 14 15
CONECT 13 12
CONECT 14 12
CONECT 15 5 12 17 16
CONECT 16 15
CONECT 17 15 55 54
CONECT 18 54
CONECT 19 21 20 31 54
CONECT 20 19
CONECT 21 19 27 22 23
CONECT 22 21
CONECT 23 21 24 26 25
CONECT 24 23
CONECT 25 23
CONECT 26 23
CONECT 27 21 30 28 29
CONECT 28 27
CONECT 29 27
CONECT 30 27
CONECT 31 19 32 32 33
CONECT 32 31 31
CONECT 33 31 34 35
CONECT 34 33
CONECT 35 33 50 36 37
CONECT 36 35
CONECT 37 35 40 39 38
CONECT 38 37
CONECT 39 37
CONECT 40 37 42 41 43
CONECT 41 40
CONECT 42 40
CONECT 43 40 46 45 44
CONECT 44 43
CONECT 45 43
CONECT 46 43 49 47 48
CONECT 47 46
CONECT 48 46
CONECT 49 46
CONECT 50 35 52 51 51
CONECT 51 50 50
CONECT 52 50 53
CONECT 53 52
CONECT 54 17 18 19
CONECT 55 17
MASTER 0 0 0 0 0 0 0 0 55 0 55 0
END

On Sep 22, 2010, at 2:59 PM, Prashanth Athri wrote: > The problem I face is
that since these atoms are new, the torsion constraint dialog box [Extensions >
Molecular Mechanics > Constraints; Type = Torsion angle] will not let me add one
of these new atoms – It does not know that they have been added and cannot
count beyond the original atom ID’s. This is true even if I re-open the file
after saving it, or re-start Avogadro. Well, I’d ordinarily say it’s a bug and
have some idea where the bug is… But I’m very surprised when you say it can’t
handle new atoms after saving and restarting Avogadro. The other problem, is
that I can’t reproduce it. I can add constraints, add more atoms, and new
constraints with the new atoms, etc. What version of Avogadro are you using?
What OS? Can you send us the file you’re trying? Thanks very much, -Geoff

–
Prashanth Athri

2

Hello,

I having the following issue:

I want to edit a molecule, as in delete some atoms and replace them with some
other. Once I do that, I want to apply torsional constraints (involving the new
atoms) and then minimize.

The problem I face is that since these atoms are new, the torsion constraint
dialog box [Extensions > Molecular Mechanics > Constraints; Type = Torsion
angle] will not let me add one of these new atoms – It does not know that they
have been added and cannot count beyond the original atom ID’s. This is true
even if I re-open the file after saving it, or re-start Avogadro.

Since the View Menu’s Torsion Properties immediately updates and displays these
new torsions, I was wondering if there is a quick way to make those updates to
the torsion angle constraint drop downs as well.

Or maybe there is another way to do this?

Thanks in advance for your response – I appreciate it.

Prashanth Athri

3

On Sep 22, 2010, at 2:59 PM, Prashanth Athri wrote:

The problem I face is that since these atoms are new, the torsion constraint dialog box [Extensions > Molecular Mechanics > Constraints; Type = Torsion angle] will not let me add one of these new atoms – It does not know that they have been added and cannot count beyond the original atom ID’s. This is true even if I re-open the file after saving it, or re-start Avogadro.

Well, I’d ordinarily say it’s a bug and have some idea where the bug is… But I’m very surprised when you say it can’t handle new atoms after saving and restarting Avogadro.

The other problem, is that I can’t reproduce it. I can add constraints, add more atoms, and new constraints with the new atoms, etc.

What version of Avogadro are you using? What OS? Can you send us the file you’re trying?

Thanks very much,
-Geoff

4

I am trying to freeze atom ID numbers: 18-54-17-55
54, 55 are the newly added atoms.

Ok, this is definitely a bug. Sorry to take a while to get back to you, but it was hard to figure out what was wrong. There are a few issues:

  1. The atom indexes in the constraints box are numbered from 0. So you’d want 17-53-16-54.
  2. The up-and-down arrows seem limited, but you can manually type numbers into the boxes.

So I entered the constraint above (17-53-16-54) and was able to enforce a constraint.

I’m going to fix both of these bugs for 1.1.

Thanks very much,
-Geoff