From: Brian Bennion (bennion1_at_llnl.gov)
Date: Thu Oct 26 2006 - 11:29:00 CDT
Hi Meric,
There are more places than residue 270 that there are clashes. DNA
residue 294 and protein 156 are interleaved and therefore NAMD is
trying to pull/rotate several atoms through defined residues.
One way to check for these complete overlaps is to read the pdb file
into vmd without the psf file. VMD will guess bond structure by a
distance based algorithm. If atoms are just too close to each other
an error stating residue blah has more than X bonds.
Another sanity check is to remove the dna from the system and just
minimize the protein for a few steps.
Brian
At 08:58 AM 10/26/2006, you wrote:
>Brian,
>sorry to bother again, I turned off the boundary conditions and also
>increased the cut-off distance non of it helped. I am sending you
>pdf and psf files, it seems only there are couple clashed atoms
>around residue 270 with dna structure. I moved manually residue 270
>but did not help.
>Meric
>On 10/26/06, Brian Bennion <<mailto:bennion1_at_llnl.gov>
>bennion1_at_llnl.gov> wrote:
>Turn off the boundary conditions for minimization as a check.
>
>
>
>
>At 08:32 AM 10/26/2006, you wrote:
>>Brian thank you very much, I did subscribe and recieved one mail
>>sent by an individual today. but my message does not appear. anyhow
>>I am using spherical boundary conditions, and using vmd's mass
>>center values. thank you for your reply, I'll keep looking.
>>Meric
>>
>>On 10/26/06, Brian Bennion
>><<mailto:bennion1_at_llnl.gov>bennion1_at_llnl.gov> wrote:
>>Hello Meric,
>>Did you "subscribe" to the namd email list? It is a two step process.
>>My initial guess is that your system is being cut by a box boundary
>>or isn't centered properly in the box you have defined.
>>Next would be increasing your cutoff value.
>>Most times one sees a 999999 in the vdw column and it is easily
>>overcome. However, its the angle and boundary value that are the clues here.
>>Brian
>>At 08:14 AM 10/26/2006, you wrote:
>> >Hi brian,
>> >I tried to post this message to namd mailing list but somehow I could not.
>> >
>> >
>> >-----Original Message-----
>> >
>> > > Date: Thu Oct 26 11:06:02 EDT 2006
>> > > From: "Meric Ovacik" <
>> <mailto:movacik_at_eden.rutgers.edu>movacik_at_eden.rutgers.edu >
>> > > Subject: GRADIENT TOLERANCE: nan
>> > > To: <mailto:namd-l_at_ks.uiuc.edu>namd-l_at_ks.uiuc.edu
>> > >
>> > >
>> > >
>> > >
>> > >
>> > >
>> > > Hi all,
>> > > > I am trying to minimize a protein and dna complex which I have
>> > created. However, I have error message as follows.
>> > > > I checked the structure, it seems there are couple clashed
>> > atoms around residue 270 with dna structure. I moved manually
>> > residue 270 but did not help.
>> > > > I would appreciate any help.
>> > > > Thank you
>> > > > meric
>> > > > ps: I tried to attach the files that I have used but the mail
>> > could not be delivered.
>> > > >
>> > > >
>> > > > TCL: Minimizing for 100 steps
>> > > > PRESSURE: 0 0 0 0 0 0 0 0 0 0
>> > > > GPRESSURE: 0 0 0 0 0 0 0 0 0 0
>> > > >
>> > ETITLE: TS BOND ANGLE DIHED
>> > IMPRP ELECT VDW BOUNDARY
>> > MISC KINETIC TOTAL TEMP
>> > TOTAL2 TOTAL3 TEMPAVG
>> > > >
>> > ENERGY: 0 18084.1897 99999999.9999 1382.0782
>> > 83.7910 -97826.6419 99999999.9999 24293334.4334
>> > 0.0000 0.0000 99999999.9999 0.0000
>> > 99999999.9999 99999999.9999 0.0000
>> > > >
>> > > > INITIAL STEP: 1e-06
>> > > > GRADIENT TOLERANCE: nan
>> > > > BRACKET: 0 nan nan nan nan
>> > > > RESTARTING CONJUGATE GRADIENT ALGORITHM
>> > > > INITIAL STEP: 5e-07
>> > > > GRADIENT TOLERANCE: nan
>> > > > BRACKET: 0 nan nan nan nan
>> > > > RESTARTING CONJUGATE GRADIENT ALGORITHM
>> > > > INITIAL STEP: 2.5e-07
>> > > > GRADIENT TOLERANCE: nan
>> > > > BRACKET: 0 nan nan nan nan
>> > > > NEW SEARCH DIRECTION
>> > > > INITIAL STEP: 1.25e-07
>> > > > GRADIENT TOLERANCE: nan
>> > >
>> >
>> >
>> >==================================================================
>> =========
>> >
>> >WARNING: This email violated LLNL's email security policy and
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>> >
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>> >An attachment named merocan_ws.zip was removed from this document as it
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>>
>>
>>
>>--
>>Meric
>
>
>
>
>--
>Meric
>Content-Type: chemical/x-pdb; name=merocan_ws.pdb
>X-Attachment-Id: f_etrcbqvl
>Content-Disposition: attachment; filename="merocan_ws.pdb"
>
>Content-Type: application/octet-stream; name=merocan_ws.psf
>X-Attachment-Id: f_etrcbwd2
>Content-Disposition: attachment; filename="merocan_ws.psf"
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