VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Aug 12 2006 - 17:29:49 CDT

Actually, now that I think about it, does an H - H - O angle even
make sense?

Can you include the topology you used to build it? (just the
modified part should be sufficient).

On Aug 12, 2006, at 5:08 PM, sseefeld_at_uwm.edu wrote:

> I edited this value to what you had suggested and I still was
> getting the same
> issue. I'm still quite baffled.
>
> Reguards, Sean Seefeld
> --
> Sean Seefeld
> University of Wisconsin - Milwaukee
> 3210 N. Cramer Street
> Milwaukee, WI 53211-3029
> sseefeld_at_uwm.edu
>
>
> Quoting JC Gumbart <gumbart_at_ks.uiuc.edu>:
>
>> The angle still essentially doesn't exist since that inserted line
>> gives it
>> a force constant of zero.
>>
>> Try this (obviously, k = 50 is just a guess, based on all other k-
>> thetas):
>>
>> HT HT OT 50.0 127.74
>>
>> Hopefully with this you will have a simulation that runs at least.
>>
>>
>> -----Original Message-----
>> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
>> Behalf Of
>> sseefeld_at_uwm.edu
>> Sent: Saturday, August 12, 2006 11:51 AM
>> To: vmd-l_at_ks.uiuc.edu
>> Subject: vmd-l: NAMD minimization error
>>
>> I modified my wild type cytochrome c by putting the TML at
>> position 72 and
>> solvating the protein with a water box using this script.
>>
>> package require psfgen
>>
>> topology top_all27_prot_lipid_ycc.inp
>>
>> pdbalias residue HEM HEME
>>
>> pdbalias residue HOH TIP3
>>
>> segment B {pdb 2YCC.pdb
>>
>> mutate 72 TML}
>>
>> coordpdb 2YCC.pdb B
>>
>> guesscoord
>>
>> writepdb 2YCCtml.pdb
>>
>> writepsf 2YCCtml.psf
>>
>> package require solvate
>>
>> solvate 2YCCtml.psf 2YCCtml.pdb -t 7 -o 2YCCtml_wb
>>
>> The min max came out as
>> {-21.3059997559 -6.99700021744 -20.3220005035} {29.9920005798
>> 44.0239982605
>> 32.9550018311}
>>
>> meaning the center is approx
>> 4.343 18.5135 6.3165
>>
>>
>> using this i setup my namd minimization
>>
>> # input
>> structure 2YCCtml_wb.psf
>> coordinates 2YCCtml_wb.pdb
>> paraTypeCharmm on
>> parameters par_all27_prot_lipid_ycc.inp
>>
>> numsteps 100
>> minimization on
>>
>> # force field parameters
>> exclude scaled1-4
>> 1-4scaling 1.0
>> cutoff 14.0
>> switching On
>> switchdist 12.0
>> pairlistdist 16.0
>>
>> # integrator params
>> timestep 1.0
>> nonbondedFreq 2
>> fullElectFrequency 4
>> stepspercycle 20
>>
>> # Periodic boundary condition
>> cellBasisVector1 48 0 0
>> cellBasisVector2 0 48 0
>> cellBasisVector3 0 0 48
>> cellorigin 4.3 18.5 6.3
>> wrapWater on
>> wrapAll on
>> wrapNearest on
>>
>> # output
>> outputname 2YCCtml_wb_min.pdb
>> dcdfile 2YCCtml_wb_min.dcd
>>
>> binaryoutput no
>> outputEnergies 100
>> dcdfreq 100
>>
>> This gives me the
>>
>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
>>
>> I looked on the mailing list and I couldn't find a solution for
>> that other
>> than
>> using a diffent program. So I decided to find a parameter file
>> that did have
>> this bond specified because I was not interested in the validity
>> of my data
>> just yet but more in seeing if I could get this to running at the
>> moment.
>>
>> I grabbed this line from
>> http://www.cs.washington.edu/homes/tapan/projects/GBP/figures/
>> PARM.PRM which
>> i
>> simply found using a google search.
>> HT HT OT 0.0 127.74
>>
>> When I now run the simulation with this new parameter file I get
>> my terminal
>> screen entirely filled with
>>
>> INITIAL STEP: 1e-300
>> GRADIENT TOLERANCE: nan
>> BRACKET: 0 0 nan nan nan
>> NEW SEARCH DIRECTION
>>
>> Over and over again so fast that I cannot see anything that
>> happens before
>> it.
>> Any help in resolving this issue to help me keep moving forward
>> would be
>> greatly appreciated.
>>
>> Thanks in advance,
>> Sean Seefeld
>>
>>