Re: problem with NAMD RNA run

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 06 2007 - 18:38:09 CST

Hi Sam,
you need to specify proper terminal patches for your RNA, or else the
default patches (NTER and CTER) will be applied. Try the following
modification to your psfgen script:

segment U {
    pdb ubqp.pdb
    first 5PHO
    last 3TER
}
coordpdb ubqp.pdb U
guesscoord
writepdb ubq.pdb

You can have a look in the topology file for full definitions of these
patches.

Best,
Peter

Samuel Coulbourn Flores wrote:
> 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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