VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Apr 19 2016 - 17:09:00 CDT

Ok. Now its clearer what is going on. You don't have a residue 1. You
have a residue 01 in the psf, and a resid 1 in the pdb. I'm not sure how
that happened, but that mismatch is the root of your problem. You should
also never say "first none" and "last none" for a protein segment. Your
chain termini are wrong as a result, and chains are ending in chemically
impossible states.

-Josh

On 04/19/2016 04:49 PM, Olya Kravchenko wrote:
> Hi Josh and Ashar, thank you for replying.
>
> coordpdb produces the following errors:
>
>> Main< (ferritin_new) 55 % coordpdb ferritin.pdb
> psfgen) reading coordinates from pdb file ferritin.pdb
> psfgen) no residue 1 of segment AF
> psfgen) Warning: failed to set coordinate for atom N THR:1 AF
> psfgen) no residue 1 of segment AF
> psfgen) Warning: failed to set coordinate for atom HN THR:1 AF
> psfgen) no residue 1 of segment AF
> psfgen) Warning: failed to set coordinate for atom CA THR:1 AF
> psfgen) no residue 1 of segment AF
>
> I attach my pdb files: 0ps.pdb is the original file that I split into
> chains before creating ferritin.pdb. I just made the structure file
> from scratch one more time (i.e. split 0ps.pdb into chains and then
> put it together with psfgen) and I have warnings for hydrogens (but no
> errors):
>
> Info: guessing coordinates for 32472 atoms (0 non-hydrogen)
> psfgen) Warning: poorly guessed coordinates for 24 atoms (0 non-hydrogen):
> psfgen) Warning: poorly guessed coordinate for atom HN THR:01 AF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:173 BF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:345 CF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:517 DF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:689 EF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:861 FF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:1033 GF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:1205 HF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:1377 IF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:1549 JF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:1721 KF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:1893 LF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:2065 MF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:2237 NF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:2409 OF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:2581 PF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:2753 QF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:2925 RF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:3097 SF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:3269 TF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:3441 UF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:3613 VF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:3785 WF
> psfgen) Warning: poorly guessed coordinate for atom HN THR:3957 XF
>
> Just in case here is the script I used to create psf file:
>
> package require psfgen
> topology toppar/top_all36_prot.rtf
>
> pdbalias atom ILE H HN
> pdbalias atom THR H HN
> pdbalias atom SER H HN
> pdbalias atom GLN H HN
> pdbalias atom VAL H HN
> pdbalias atom ARG H HN
> pdbalias atom ASN H HN
> pdbalias atom TYR H HN
> pdbalias atom HIS H HN
> pdbalias atom ASP H HN
> pdbalias atom GLU H HN
> pdbalias atom ALA H HN
> pdbalias atom GLY O1 O
> pdbalias atom GLY O2 O
> pdbalias residue HIS HSD
> pdbalias atom HSD CD1 CD
> pdbalias atom ILE CD1 CD
>
> segment AF {
> first NONE
> last NONE
> pdb chainA.pdb
> }
>
> segment BF {
> first NONE
> last NONE
> pdb chainB.pdb
> }
>
> segment CF {
> first NONE
> last NONE
> pdb chainC.pdb
> }
>
> segment DF {
> first NONE
> last NONE
> pdb chainD.pdb
> }
>
> segment EF {
> first NONE
> last NONE
> pdb chainE.pdb
> }
>
> segment FF {
> first NONE
> last NONE
> pdb chainF.pdb
> }
>
> segment GF {
> first NONE
> last NONE
> pdb chainG.pdb
> }
>
> segment HF {
> first NONE
> last NONE
> pdb chainH.pdb
> }
>
> segment IF {
> first NONE
> last NONE
> pdb chainI.pdb
> }
>
> segment JF {
> first NONE
> last NONE
> pdb chainJ.pdb
> }
>
> segment KF {
> first NONE
> last NONE
> pdb chainK.pdb
> }
>
> segment LF {
> first NONE
> last NONE
> pdb chainL.pdb
> }
>
> segment MF {
> first NONE
> last NONE
> pdb chainM.pdb
> }
>
> segment NF {
> first NONE
> last NONE
> pdb chainN.pdb
> }
>
> segment OF {
> first NONE
> last NONE
> pdb chainO.pdb
> }
>
> segment PF {
> first NONE
> last NONE
> pdb chainP.pdb
> }
>
> segment QF {
> first NONE
> last NONE
> pdb chainQ.pdb
> }
>
> segment RF {
> first NONE
> last NONE
> pdb chainR.pdb
> }
>
> segment SF {
> first NONE
> last NONE
> pdb chainS.pdb
> }
>
> segment TF {
> first NONE
> last NONE
> pdb chainT.pdb
> }
>
> segment UF {
> first NONE
> last NONE
> pdb chainU.pdb
> }
>
> segment VF {
> first NONE
> last NONE
> pdb chainV.pdb
> }
>
> segment WF {
> first NONE
> last NONE
> pdb chainW.pdb
> }
>
> segment XF {
> first NONE
> last NONE
> pdb chainX.pdb
> }
>
> coordpdb chainA.pdb AF
> coordpdb chainB.pdb BF
> coordpdb chainC.pdb CF
> coordpdb chainD.pdb DF
> coordpdb chainE.pdb EF
> coordpdb chainF.pdb FF
> coordpdb chainG.pdb GF
> coordpdb chainH.pdb HF
> coordpdb chainI.pdb IF
> coordpdb chainJ.pdb JF
> coordpdb chainK.pdb KF
> coordpdb chainL.pdb LF
> coordpdb chainM.pdb MF
> coordpdb chainN.pdb NF
> coordpdb chainO.pdb OF
> coordpdb chainP.pdb PF
> coordpdb chainQ.pdb QF
> coordpdb chainR.pdb RF
> coordpdb chainS.pdb SF
> coordpdb chainT.pdb TF
> coordpdb chainU.pdb UF
> coordpdb chainV.pdb VF
> coordpdb chainW.pdb WF
> coordpdb chainX.pdb XF
>
> writepsf ferritin.psf
>
> guesscoord
> writepdb ferritin.pdb
>
> Thank you!
>
> Olga
>
>
>
>
> On Tue, Apr 19, 2016 at 5:27 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
>> Hi Olya,
>>
>> Thats a weird error, and one I haven't seen before. What solvate is supposed
>> to do is read in your original psf pdb pair, construct a sufficiently large
>> waterbox, put the two together, and carve out waters that are too close to
>> the solute. Unfortunately, it does so by calling psfgen, which apparently
>> doesn't like something about how the system is put together when it reads in
>> the psf and thinks you don't have a residue 1 of segment A, and refuses to
>> set coordinates accordingly. What you could do to avoid this is to build a
>> waterbox alone, merge the two systems together using topotools, and remove
>> the waters using an atomselection:
>>
>> set sel [atomselect top "(not water) or (water and not same residue as (name
>> OH2 and within 2.4 of (not water)))"]
>> $sel writepsf blah.psf
>> $sel writepdb blah.pdb
>>
>> The trouble with this approach is that you'll face the same problem during
>> ionization (probably), so you should probably figure out why psfgen is
>> misbehaving. Does something simple like:
>>
>> readpsf ferritin.psf
>> coordpdb ferritin.pdb
>>
>> writepsf test.psf
>> writepdb test.pdb
>>
>> work at all? Or does this also throw errors?
>>
>> -Josh Vermaas
>>
>>
>> On 04/19/2016 02:59 PM, Olya Kravchenko wrote:
>>> Hi all,
>>>
>>> I am trying to solvate ferritin (it is a spherical molecule that
>>> consists of 24 identical chains, 66456 atoms ) in a water box and keep
>>> getting the same error regardless of whether I run it in a tcl/tk
>>> console or graphic interface. The error is only for the first 9
>>> residues of the first chain, total of 151 atoms. When I run solvate,
>>> i.e.
>>>
>>> package require solvate
>>> solvate ferritin.psf ferritin.pdb -t 5 -o solvated
>>>
>>> I see warnings such as these:
>>>
>>> psfgen) no residue 1 of segment A
>>> psfgen) Warning: failed to set coordinate for atom N THR:1 A
>>> psfgen) no residue 1 of segment A
>>> psfgen) Warning: failed to set coordinate for atom HN THR:1 A
>>> psfgen) no residue 1 of segment A
>>> psfgen) Warning: failed to set coordinate for atom CA THR:1 A
>>> psfgen) no residue 1 of segment A
>>> psfgen) Warning: failed to set coordinate for atom HA THR:1 A
>>> psfgen) no residue 1 of segment A
>>> psfgen) Warning: failed to set coordinate for atom CB THR:1 A
>>> ..
>>> ..
>>>
>>> and so on for the next 151 atoms in a ferritin.pdb file.
>>>
>>> When the file solvated.pdb is created, the first 151 atoms have zero
>>> coordinates:
>>>
>>> ATOM 1 N THR A 1 0.000 0.000 0.000 -1.00 0.00 A
>>> ATOM 2 HN THR A 1 0.000 0.000 0.000 -1.00 0.00 A
>>> ATOM 3 CA THR A 1 0.000 0.000 0.000 -1.00 0.00 A
>>> ATOM 4 HA THR A 1 0.000 0.000 0.000 -1.00 0.00 A
>>> ATOM 5 CB THR A 1 0.000 0.000 0.000 -1.00 0.00 A
>>> ..
>>> ..
>>>
>>> In the ferritin.pdb file the same atoms have coordinates and and look
>>> normal in VMD before I solvate the structure:
>>>
>>>
>>> ATOM 1 N THR A 1 29.972 78.277 67.795 1.00 0.00 A
>>> ATOM 2 HN THR A 1 30.255 79.195 67.517 0.00 0.00 A
>>> ATOM 3 CA THR A 1 30.644 77.930 69.037 1.00 0.00 A
>>> ATOM 4 HA THR A 1 30.049 78.354 69.834 0.00 0.00 A
>>> ATOM 5 CB THR A 1 30.648 76.421 69.061 1.00 0.00 A
>>> ..
>>> ..
>>>
>>> I don't understand what causes this error and why only on the first 9
>>> residues of the very first chain?
>>>
>>> I searched the archives, but did not find a similar issue being
>>> discussed. Initially I thought there may be non-standard atom or
>>> residue names that do not correspond to those in the parameter files,
>>> but all seems to be consistent, and in any case I do not see errors of
>>> this sort for the rest of the molecules even though the chains are
>>> identical (and so are atom and residue names). I use
>>> top_all36_prot.rtf for topology.
>>>
>>> I'd very much appreciate your input!
>>>
>>> Olga
>>>