Re: problem with NAMD RNA run

From: Samuel Coulbourn Flores (scflores_at_stanford.edu)
Date: Tue Nov 06 2007 - 20:53:51 CST

Excellent! this is running nicely now.

Sam

On Nov 6, 2007, at 4:38 PM, Peter Freddolino wrote:

> 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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