VMD-L Mailing List
From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Tue Apr 19 2016 - 14:59:01 CDT
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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
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- Previous message: Laura Joana: "Re: colvars problem - different values in VMD and NAMD"
- Next in thread: Josh Vermaas: "Re: solvate fails to set coordinates for the first few residues of the first chain?"
- Reply: Josh Vermaas: "Re: solvate fails to set coordinates for the first few residues of the first chain?"
- Reply: Ashar Malik: "Re: solvate fails to set coordinates for the first few residues of the first chain?"
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