VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Jan 06 2022 - 15:27:37 CST

Because you didn't post bond information there's no way for us to help on
this point. Can you send at least a segment of the output pdb/psf that
illustrates the issue? Ideally also the topology file(s) that you used.
Thanks,
Peter

On Thu, Jan 6, 2022 at 3:28 PM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Hi Peter
> Yes, for the phosphate oxygens that was clear from the fact that
> connection between standard nucleotides was treated correctly despite the
> atom name mismatch.
>
> For connections with modified nucleotides the problem remains. It seems
> that the current code does not know them, or treat them as if they were
> nucleosides.
>
> Thanks
> francesco
>
> On Thu, Jan 6, 2022, 7:13 PM Peter Freddolino <petefred_at_umich.edu> wrote:
>
>> There is a set of aliases in autopsf that handle the OP1/etc naming
>> because many pdbs follow this convention:
>> foreach bp { GUA CYT ADE THY URA } {
>> pdbalias atom $bp "O5\*" O5'
>> pdbalias atom $bp "C5\*" C5'
>> pdbalias atom $bp "O4\*" O4'
>> pdbalias atom $bp "C4\*" C4'
>> pdbalias atom $bp "C3\*" C3'
>> pdbalias atom $bp "O3\*" O3'
>> pdbalias atom $bp "C2\*" C2'
>> pdbalias atom $bp "O2\*" O2'
>> pdbalias atom $bp "C1\*" C1'
>> pdbalias atom $bp "OP1" O1P
>> pdbalias atom $bp "OP2" O2P
>> }
>>
>> But similar aliases would be needed for any custom residue that should
>> behave similarly.
>> Thanks,
>> Peter
>>
>> On Thu, Jan 6, 2022 at 10:02 AM Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>>> With the standard nucleotides, psfgen takes OP1 and OP2 as O1P and O2P,
>>> respectively, and inserts them into the structures. Does that mean that
>>> psfgen looks heuristically at the residues name? If so, why not for the
>>> modified nucleosides?
>>> f
>>>
>>> ---------- Forwarded message ---------
>>> From: Francesco Pietra <chiendarret_at_gmail.com>
>>> Date: Thu, Jan 6, 2022 at 9:45 AM
>>> Subject: Re: vmd-l: Failure of autopsf with modified nucleotides
>>> To: Peter Freddolino <petefred_at_umich.edu>
>>> Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>>>
>>>
>>> Hi Peter
>>> Very sorry for having overlooked both the name mismatch and the missing
>>> atoms
>>>
>>> As to the latter problem, I should learn where to find missing atoms in
>>> .cif files. With the way I used to change .cif into .pdb (through chimeraX
>>> software) such information is lost
>>>
>>> Thanks a lot for your advice
>>> francesco
>>>
>>> On Thu, Jan 6, 2022, 2:55 PM Peter Freddolino <petefred_at_umich.edu>
>>> wrote:
>>>
>>>> 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
>>>>>
>>>>