From: Samuel Coulbourn Flores (scflores_at_stanford.edu)
Date: Tue Nov 06 2007 - 18:31:04 CST
Hi Brittany,
I would also think this could cause such errors. However upon taking
a closer look I found that vmd was trying to turn my RNA into a
protein! The ubq.pdb file has some protein-backbone-like atoms
inserted. I've appended the contents of 1UBQ.pdb and ubq.pdb below.
The segment or writepdb commands are at fault, commenting out
coordpdb and guesscoord doesn't help:
segment U {pdb ubqp.pdb}
coordpdb ubqp.pdb U
guesscoord
writepdb ubq.pdb
Can you tell me how to properly prepare an RNA file for a NAMD run?
Many thanks
Sam
clark-alt-wi-2:~/tbss.work/work samuelflores$ cat 1UBQ.pdb
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 O5' U A2647 26.832 -3.731 16.487 1.00
22.26 O
ATOM 2 C5' U A2647 27.875 -2.872 17.009 1.00
21.79 C
ATOM 3 C4' U A2647 27.337 -2.101 18.176 1.00
21.61 C
ATOM 4 O4' U A2647 28.352 -1.522 19.037 1.00
21.49 O
ATOM 5 C3' U A2647 26.410 -0.929 17.857 1.00
21.47 C
ATOM 6 O3' U A2647 25.170 -1.388 17.380 1.00
21.48 O
ATOM 7 C2' U A2647 26.311 -0.325 19.262 1.00
21.43 C
ATOM 8 O2' U A2647 25.577 -1.148 20.153 1.00
21.37 O
ATOM 9 C1' U A2647 27.802 -0.350 19.642 1.00
21.37 C
ATOM 10 N1 U A2647 28.531 0.795 19.072 1.00
21.16 N
ATOM 11 C2 U A2647 28.201 2.068 19.496 1.00
21.05 C
ATOM 12 O2 U A2647 27.327 2.315 20.313 1.00
20.84 O
ATOM 13 N3 U A2647 28.926 3.075 18.908 1.00
20.92 N
ATOM 14 C4 U A2647 29.930 2.945 17.972 1.00
20.92 C
ATOM 15 O4 U A2647 30.493 3.958 17.556 1.00
20.79 O
ATOM 16 C5 U A2647 30.188 1.600 17.569 1.00
20.97 C
ATOM 17 C6 U A2647 29.528 0.588 18.145 1.00
21.10 C
clark-alt-wi-2:~/tbss.work/work samuelflores$ cat ubq.pdb
REMARK original generated coordinate pdb file
ATOM 1 C URA A2647 0.000 0.000 0.000 -1.00
0.00 U C
ATOM 2 OT1 URA A2647 0.000 0.000 0.000 -1.00
0.00 U O
ATOM 3 OT2 URA A2647 0.000 0.000 0.000 -1.00
0.00 U O
ATOM 4 N URA A2647 0.000 0.000 0.000 -1.00
0.00 U N
ATOM 5 HT1 URA A2647 0.000 0.000 0.000 -1.00
0.00 U H
ATOM 6 HT2 URA A2647 0.000 0.000 0.000 -1.00
0.00 U H
ATOM 7 HT3 URA A2647 0.000 0.000 0.000 -1.00
0.00 U H
ATOM 8 CA URA A2647 0.000 0.000 0.000 -1.00
0.00 U C
ATOM 9 HA URA A2647 0.000 0.000 0.000 -1.00
0.00 U H
ATOM 10 P URA A2647 27.242 -5.097 15.762 0.00
0.00 U P
ATOM 11 O1P URA A2647 26.420 -5.647 15.615 0.00
0.00 U O
ATOM 12 O2P URA A2647 28.171 -5.358 15.499 0.00
0.00 U O
ATOM 13 O5' URA A2647 26.832 -3.731 16.487 1.00
0.00 U O
ATOM 14 C5' URA A2647 27.875 -2.872 17.009 1.00
0.00 U C
ATOM 15 H5' URA A2647 28.110 -2.189 16.318 0.00
0.00 U H
ATOM 16 H5'' URA A2647 28.612 -3.440 17.376 0.00
0.00 U H
ATOM 17 C4' URA A2647 27.337 -2.101 18.176 1.00
0.00 U C
ATOM 18 H4' URA A2647 26.814 -2.775 18.697 0.00
0.00 U H
ATOM 19 O4' URA A2647 28.352 -1.522 19.037 1.00
0.00 U O
ATOM 20 C1' URA A2647 27.802 -0.350 19.642 1.00
0.00 U C
ATOM 21 H1' URA A2647 27.884 -0.467 20.632 0.00
0.00 U H
ATOM 22 N1 URA A2647 28.531 0.795 19.072 1.00
0.00 U N
ATOM 23 C6 URA A2647 29.528 0.588 18.145 1.00
0.00 U C
ATOM 24 H6 URA A2647 29.883 -0.277 17.789 0.00
0.00 U H
ATOM 25 C2 URA A2647 28.201 2.068 19.496 1.00
0.00 U C
ATOM 26 O2 URA A2647 27.327 2.315 20.313 1.00
0.00 U O
ATOM 27 N3 URA A2647 28.926 3.075 18.908 1.00
0.00 U N
ATOM 28 H3 URA A2647 28.692 4.034 19.201 0.00
0.00 U H
ATOM 29 C4 URA A2647 29.930 2.945 17.972 1.00
0.00 U C
ATOM 30 O4 URA A2647 30.493 3.958 17.556 1.00
0.00 U O
ATOM 31 C5 URA A2647 30.188 1.600 17.569 1.00
0.00 U C
ATOM 32 H5 URA A2647 30.885 1.603 16.852 0.00
0.00 U H
ATOM 33 C2' URA A2647 26.311 -0.325 19.262 1.00
0.00 U C
ATOM 34 H2'' URA A2647 25.991 0.620 19.188 0.00
0.00 U H
ATOM 35 O2' URA A2647 25.577 -1.148 20.153 1.00
0.00 U O
ATOM 36 H2' URA A2647 25.856 -1.102 21.070 0.00
0.00 U H
ATOM 37 C3' URA A2647 26.410 -0.929 17.857 1.00
0.00 U C
ATOM 38 H3' URA A2647 26.883 -0.298 17.242 0.00
0.00 U H
ATOM 39 O3' URA A2647 25.170 -1.388 17.380 1.00
0.00 U O
END
clark-alt-wi-2:~/tbss.work/work samuelflores$
On Nov 6, 2007, at 2:03 PM, Brittany Morgan wrote:
> All of the messages starting with “Info:” appear to be normal
> messages listing the simulation parameters (the minimization is
> where it is getting stuck, so a lot of these parameters aren’t
> relevant right now). However, having infinite (NaN) pressure and
> energies that exceed the maximum is why you are unable to minimize
> your system. NAMD will keep reducing the gradient tolerance in an
> attempt to minimize, but it usually is unsuccessful when the system
> starts so far out of equilibrium. As to why this is happening, it
> is likely an issue with unrealistic bond lengths or overlapping van
> der Waals radii. How did you set up the G residue in the water box?
> Is the system electrostatically neutral? You could also try
> manually checking your input files to make sure all the atoms in
> the residue are connected properly (psfgen sometimes messes this up).
>
>
>
> I attempted to reply through the list to your previous email, but
> it doesn’t seem to have gone through. Maybe it will eventually, so
> rather than spam the list, I thought I’d try emailing you directly
> first.
>
>
>
> Brittany Morgan
>
>
>
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