VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Apr 19 2016 - 16:17:17 CDT

Could you send over the pdb file please?
On Apr 20, 2016 8:32 AM, "Olya Kravchenko" <ovkrav_at_gmail.com> 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
>
>