VMD-L Mailing List

From: sseefeld_at_uwm.edu
Date: Sat Aug 12 2006 - 18:45:17 CDT

I hadn't thought of the topology file being the issue, but now that you bring it
up i was trying to fix the wrong file.

Here are the two topology entries for the waters.

RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral

GROUP

ATOM OH2 OT -0.834

ATOM H1 HT 0.417

ATOM H2 HT 0.417

BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake

ANGLE H1 OH2 H2 ! required

ACCEPTOR OH2

PATCHING FIRS NONE LAST NONE

RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p

GROUP

ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup

ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup

ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup

BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake
with tip3p

ANGLE H1 OH2 H2 ! required

ACCEPTOR OH2

PATCHING FIRS NONE LAST NONE

I should be doing pdb alias residue HOH TP3M not TIP3 because the TIP3 is
setting up the H1 H2 bond. Where as the TP3M is just the two O-H bonds. This
makes my earlier modification to the parameter file useless. I'm going to try
this quick and then reply again.

Thanks,
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>:
> 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
> >>
> >>
>
>