VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Jan 06 2022 - 07:55:42 CST

Hi Francesco,
At least part of the problem is a mismatch in atom naming between your
input PDB and the topology. For example, your input has phosphate oxygens
named "OP1" and "OP2", but the topology appears to instead have phosphate
oxygens named "O1P" and "O2P". You should not be surprised that psfgen is
having trouble placing the atoms given that many of them are effectively
missing in the input file. You either need to rename your input atoms to
match the topologies, or set up appropriate aliases.
Best,
Peter

On Thu, Jan 6, 2022 at 5:20 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Hello
> It occurs to me that autopsf fails with RNA stretches containing both
> standard and modified nucleosides OMA OMG OMC 3MU PSU 1MA (for which
> topologies are available, using VMD 1.9.4a55 on Debian 11 linux with latest
> CHARMM36)
>
> That is, O1P and O2P atoms for modified nucleosides are included in a long
> list of
> psfgen) Warning: poorly guessed coordinates for 107 atoms (58
> non-hydrogen):
>
> Per se such warnings should turn out ineffective if the system is built
> correctly. But in this case it is not: the phosphate group is omitted. An
> example
> Starting .pdb:
> ATOM 8611 N1 PSU N4450 245.386 271.989 245.976 1.00 32.02
> N
> ATOM 8612 C2 PSU N4450 246.531 271.461 245.425 1.00 32.02
> C
> ATOM 8613 N3 PSU N4450 246.808 270.121 245.558 1.00 32.02
> N
> ATOM 8614 C4 PSU N4450 245.938 269.314 246.246 1.00 32.02
> C
> ATOM 8615 C5 PSU N4450 244.794 269.853 246.796 1.00 32.02
> C
> ATOM 8616 C6 PSU N4450 244.528 271.203 246.653 1.00 32.02
> C
> ATOM 8617 O2 PSU N4450 247.306 272.189 244.813 1.00 32.02
> O
> ATOM 8618 O4 PSU N4450 246.170 268.117 246.371 1.00 32.02
> O
> ATOM 8619 C1' PSU N4450 243.851 268.964 247.537 1.00 32.02
> C
> ATOM 8620 C2' PSU N4450 243.903 269.220 249.036 1.00 32.02
> C
> ATOM 8621 O2' PSU N4450 244.974 268.534 249.647 1.00 32.02
> O
> ATOM 8622 C3' PSU N4450 242.523 268.735 249.469 1.00 32.02
> C
> ATOM 8623 C4' PSU N4450 241.641 269.127 248.285 1.00 32.02
> C
> ATOM 8624 O3' PSU N4450 242.552 267.313 249.568 1.00 32.02
> O
> ATOM 8625 O4' PSU N4450 242.527 269.261 247.146 1.00 32.02
> O
> ATOM 8626 C5' PSU N4450 240.827 270.389 248.442 1.00 32.02
> C
> ATOM 8627 O5' PSU N4450 241.482 271.360 249.248 1.00 32.02
> O
> ATOM 8628 P PSU N4450 241.204 272.910 249.051 1.00 32.02
> P
> ATOM 8629 OP1 PSU N4450 242.316 273.465 248.257 1.00 32.02
> O
> ATOM 8630 OP2 PSU N4450 239.811 273.074 248.589 1.00 32.02
> O
> ATOM 8631 P G N4451 242.024 266.568 250.885 1.00 31.99
> P
> ATOM 8632 OP1 G N4451 242.010 265.117 250.587 1.00 31.99
> O
> ATOM 8633 OP2 G N4451 240.785 267.235 251.349 1.00 31.99
> O
> ATOM 8634 O5' G N4451 243.162 266.831 251.965 1.00 31.99
> O
> ATOM 8635 C5' G N4451 244.373 266.089 251.953 1.00 31.99
> C
> ATOM 8636 C4' G N4451 245.262 266.477 253.105 1.00 31.99
> C
> ATOM 8637 O4' G N4451 244.583 266.207 254.354 1.00 31.99
> O
> ATOM 8638 C3' G N4451 246.577 265.726 253.225 1.00 31.99
> C
> ATOM 8639 O3' G N4451 247.582 266.263 252.385 1.00 31.99
> O
> ATOM 8640 C2' G N4451 246.905 265.852 254.705 1.00 31.99
> C
> ATOM 8641 O2' G N4451 247.489 267.115 254.976 1.00 31.99
> O
> ATOM 8642 C1' G N4451 245.514 265.818 255.336 1.00 31.99
> C
> ATOM 8643 N9 G N4451 245.142 264.480 255.827 1.00 31.99
> N
> ATOM 8644 C8 G N4451 244.450 263.512 255.151 1.00 31.99
> C
> ATOM 8645 N7 G N4451 244.260 262.435 255.856 1.00 31.99
> N
> ATOM 8646 C5 G N4451 244.863 262.710 257.072 1.00 31.99
> C
> ATOM 8647 C6 G N4451 244.988 261.920 258.239 1.00 31.99
> C
> ATOM 8648 O6 G N4451 244.573 260.776 258.446 1.00 31.99
> O
> ATOM 8649 N1 G N4451 245.676 262.590 259.239 1.00 31.99
> N
> ATOM 8650 C2 G N4451 246.181 263.856 259.134 1.00 31.99
> C
> ATOM 8651 N2 G N4451 246.817 264.333 260.209 1.00 31.99
> N
> ATOM 8652 N3 G N4451 246.073 264.602 258.055 1.00 31.99
> N
> ATOM 8653 C4 G N4451 245.410 263.969 257.070 1.00 31.99
> C
>
> Generated autopsf.pdb:
> ATOM 16729 C5 PSU N4450 244.794 269.853 246.796 1.00 0.00
> NO61 C
> ATOM 16730 C4 PSU N4450 245.938 269.314 246.246 1.00 0.00
> NO61 C
> ATOM 16731 O4 PSU N4450 246.170 268.117 246.371 1.00 0.00
> NO61 O
> ATOM 16732 N3 PSU N4450 246.808 270.121 245.558 1.00 0.00
> NO61 N
> ATOM 16733 H3 PSU N4450 247.599 269.675 245.139 0.00 0.00
> NO61 H
> ATOM 16734 C2 PSU N4450 246.531 271.461 245.425 1.00 0.00
> NO61 C
> ATOM 16735 O2 PSU N4450 247.306 272.189 244.813 1.00 0.00
> NO61 O
> ATOM 16736 N1 PSU N4450 245.386 271.989 245.976 1.00 0.00
> NO61 N
> ATOM 16737 H1 PSU N4450 245.276 272.974 245.807 0.00 0.00
> NO61 H
> ATOM 16738 C6 PSU N4450 244.528 271.203 246.653 1.00 0.00
> NO61 C
> ATOM 16739 H6 PSU N4450 243.621 271.630 247.090 0.00 0.00
> NO61 H
> ATOM 16740 P PSU N4450 241.204 272.910 249.051 1.00 0.00
> NO61 P
> ATOM 16741 O1P PSU N4450 241.969 273.551 248.989 0.00 0.00
> NO61 O
> ATOM 16742 O2P PSU N4450 240.264 273.245 248.989 0.00 0.00
> NO61 O
> ATOM 16743 O5' PSU N4450 241.482 271.360 249.248 1.00 0.00
> NO61 O
> ATOM 16744 C5' PSU N4450 240.827 270.389 248.442 1.00 0.00
> NO61 C
> ATOM 16745 H5' PSU N4450 240.741 270.743 247.511 0.00 0.00
> NO61 H
> ATOM 16746 H5'' PSU N4450 239.995 270.088 248.907 0.00 0.00
> NO61 H
> ATOM 16747 C1' PSU N4450 243.851 268.964 247.537 1.00 0.00
> NO61 C
> ATOM 16748 H1' PSU N4450 243.999 267.990 247.368 0.00 0.00
> NO61 H
> ATOM 16749 C4' PSU N4450 241.641 269.127 248.285 1.00 0.00
> NO61 C
> ATOM 16750 O4' PSU N4450 242.527 269.261 247.146 1.00 0.00
> NO61 O
> ATOM 16751 H4' PSU N4450 241.014 268.365 248.122 0.00 0.00
> NO61 H
> ATOM 16752 C2' PSU N4450 243.903 269.220 249.036 1.00 0.00
> NO61 C
> ATOM 16753 H2'' PSU N4450 243.968 270.204 249.199 0.00 0.00
> NO61 H
> ATOM 16754 O2' PSU N4450 244.974 268.534 249.647 1.00 0.00
> NO61 O
> ATOM 16755 H2' PSU N4450 245.765 268.456 249.109 0.00 0.00
> NO61 H
> ATOM 16756 C3' PSU N4450 242.523 268.735 249.469 1.00 0.00
> NO61 C
> ATOM 16757 H3' PSU N4450 242.240 269.258 250.273 0.00 0.00
> NO61 H
> ATOM 16758 O3' PSU N4450 242.552 267.313 249.568 1.00 0.00
> NO61 O
> ATOM 16759 H5T GUA N4451 242.599 266.548 251.189 0.00 0.00
> NN64 H
> ATOM 16760 O5' GUA N4451 243.162 266.831 251.965 1.00 0.00
> NN64 O
> ATOM 16761 C5' GUA N4451 244.373 266.089 251.953 1.00 0.00
> NN64 C
> ATOM 16762 H5' GUA N4451 244.895 266.332 251.135 0.00 0.00
> NN64 H
> ATOM 16763 H5'' GUA N4451 244.165 265.123 252.106 0.00 0.00
> NN64 H
> ATOM 16764 C4' GUA N4451 245.262 266.477 253.105 1.00 0.00
> NN64 C
> ATOM 16765 H4' GUA N4451 245.470 267.454 253.052 0.00 0.00
> NN64 H
> ATOM 16766 O4' GUA N4451 244.583 266.207 254.354 1.00 0.00
> NN64 O
> ATOM 16767 C1' GUA N4451 245.514 265.818 255.336 1.00 0.00
> NN64 C
> ATOM 16768 H1' GUA N4451 245.466 266.510 256.057 0.00 0.00
> NN64 H
> ATOM 16769 N9 GUA N4451 245.142 264.480 255.827 1.00 0.00
> NN64 N
> ATOM 16770 C4 GUA N4451 245.410 263.969 257.070 1.00 0.00
> NN64 C
> ATOM 16771 N2 GUA N4451 246.817 264.333 260.209 1.00 0.00
> NN64 N
> ATOM 16772 H21 GUA N4451 246.963 263.859 261.089 0.00 0.00
> NN64 H
> ATOM 16773 H22 GUA N4451 247.192 265.268 260.133 0.00 0.00
> NN64 H
> ATOM 16774 N3 GUA N4451 246.073 264.602 258.055 1.00 0.00
> NN64 N
> ATOM 16775 C2 GUA N4451 246.181 263.856 259.134 1.00 0.00
> NN64 C
> ATOM 16776 N1 GUA N4451 245.676 262.590 259.239 1.00 0.00
> NN64 N
> ATOM 16777 H1 GUA N4451 245.818 262.096 260.131 0.00 0.00
> NN64 H
> ATOM 16778 C6 GUA N4451 244.988 261.920 258.239 1.00 0.00
> NN64 C
> ATOM 16779 O6 GUA N4451 244.573 260.776 258.446 1.00 0.00
> NN64 O
> ATOM 16780 C5 GUA N4451 244.863 262.710 257.072 1.00 0.00
> NN64 C
> ATOM 16781 N7 GUA N4451 244.260 262.435 255.856 1.00 0.00
> NN64 N
> ATOM 16782 C8 GUA N4451 244.450 263.512 255.151 1.00 0.00
> NN64 C
> ATOM 16783 H8 GUA N4451 244.037 263.388 254.249 0.00 0.00
> NN64 H
> ATOM 16784 C2' GUA N4451 246.905 265.852 254.705 1.00 0.00
> NN64 C
> ATOM 16785 H2'' GUA N4451 247.414 265.042 254.996 0.00 0.00
> NN64 H
> ATOM 16786 O2' GUA N4451 247.489 267.115 254.976 1.00 0.00
> NN64 O
> ATOM 16787 H2' GUA N4451 247.302 267.469 255.848 0.00 0.00
> NN64 H
> ATOM 16788 C3' GUA N4451 246.577 265.726 253.225 1.00 0.00
> NN64 C
> ATOM 16789 H3' GUA N4451 246.421 264.761 253.016 0.00 0.00
> NN64 H
> ATOM 16790 O3' GUA N4451 247.582 266.263 252.385 1.00 0.00
> NN64 O
>
> The structural work was at 3A resolution and, on such basis, I don't see
> why such poorly guessing.
> What I can only suppose is that autopsf is using an internal guess based
> on nucleotide names and
> not including the modified nucleotides, although the topology files
> included them.
>
> Any way to come out? Perhaps forcing autopsf to look at distances between
> atoms. Thanks for advice
>
> francesco pietra
>