Update:
Preventing the system from going to steepest-descent minimization kept the
structure in a reasonable conformation.
However, once that is lifted and or md is done the entire system goes nuts.
by nuts I mean
after just a few steps of "heating" dt=0.0001 going from 0-30 deg K the
top of the rst file looks like this:
head relax.rst
default_name
1071 0.2100000E+01
-190.8380641-129.7748093 -52.1977614************************************
7849.4009899************************************************************
-162.7410150-121.9460748 11.9699740 1.3359001 47.3867081 4.5057879
-194.1214670 -75.5330836 6.7615233************************************
************************************-210.9862100 -23.4231856 -17.9718647
-253.6432364 -70.4021849 62.9167238-253.3465114 -69.4420922 63.3124287
-237.3854784-147.4313973 97.4907040-254.0803973-185.8415706 135.6059231
-136.1180124 -34.5802773 -35.2672772-135.4527532 -33.7925811 -34.9457728
after 199000
it looks like
default_name
1071 0.1805000E+02
************************************************************************
8932.9031468************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
************************************************************************
coordinates are off into infinity or something...
I didn't mention before, but will now (as I believe this is the REAL issue)
There are phosphates on a few residues. therefore I chose to use
Phosphorylated Serine and Threonine
parameters (sticht) from
http://www.pharmacy.manchester.ac.uk/bryce/amber#pro
I loaded in the frcmod and off files in leap and that created the
associated inpcrd and prmtop files
To test I created a smaller portion (that was decent in the
x-ray structure) of the over all complex and attempted a minimization and
heating to 30K. same thing happened.
The questions are:
1. Is this a known issue?
2. Could there be a problem with compatibility with ff12SB
3. Am I actually doing something wrong (misloading the off and frcmod
files, or something else) and the parameters are OK?
4. There are other parameters I could use (on the above site), but would
it be better to simply use antechamber?
5. Is there a "typical" approach (I know there are lots) to simulating
phosphates that I am just missing (since I'm a newbie)?
Again, thank you all for your patience and help,
Jonathan
On Wed, Apr 24, 2013 at 12:26 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Tue, Apr 23, 2013 at 2:47 PM, Jonathan Gough
> > <jonathan.d.gough.gmail.com>wrote:
> >
> > > I have a pdb (from an x-ray structure) that was missing several
> > > "loops"(they are floppy therefore were very disordered in the
> crystals).
> > > I used swisspdb viewer to add the residues back in but on a few of the
> > > "connections" it was a stretch.
> > >
> > > therefore leap warns me that
> > >
> > > WARNING: There is a bond of 6.802961 angstroms between:
> > > ------- .R<SER 363>.A<C 10> and .R<ARG 364>.A<N 1>
> > > WARNING: There is a bond of 3.723094 angstroms between:
> > > ------- .R<SER 990>.A<C 10> and .R<ARG 991>.A<N 1>
> > > WARNING: There is a bond of 4.437505 angstroms between:
> > > ------- .R<ALA 1197>.A<C 9> and .R<VAL 1198>.A<N 1>
>
> A situation like this begs for inspection in xleap, which has the
> useful ability to select and minimize groups of atoms (using basic
> rules and without the vdw term). The slightest knowledge of chemistry
> will often result in something that will minimize nicely in sander or
> pmemd.
>
> Note this is the only place leap's idea of bond order might matter -
> adjust by double-clicking on bonds if so.
>
> That said, low temperature dynamics will solve a lot of problems, and
> give an interesting movie no matter what.
>
> Bill
>
> > >
> > > and (of course?) there aren't any improper torsion parameters and I
> get
> > > more warnings.
> > >
> > > the question is
> > >
> > > 1 - can I still use what I have and minimize (I think I have tried this
> > > several different ways and things go crazy)? If so any suggestions on
> how
> > > to go about doing it? (I tried/thought I could do it in implicit and
> > > explicit solvent followed by slow heating with heavy constraints and
> short
> > > times steps.)
> > >
> >
> > What happens if you use strong positional restraints (~500-1000 kcal/mol)
> > on the part of the structure that started out OK and then minimize only
> > those residues that had to be 'built-in'? For such a strained structure,
> > you should set ncyc to a very large number to make sure that
> > steepest-descent minimization is used instead of switching to the
> conjugate
> > gradient minimizer after 10 steps or so.
> >
> > An alternative is to set temp0 to 0 K and run dynamics instead of
> > minimization, using a very short time step (e.g., 0.0001 or maybe even
> > lower -- try experimenting here), but I would suggest trying the
> > minimization first.
> >
> > I would do this all in implicit solvent, too, to avoid wasting time
> dealing
> > with the explicit solvent molecules. Then you can create a PDB based on
> > this structure and solvate if necessary.
> >
> > Alternatively, does SwissPDB viewer have a minimization option that may
> be
> > able to relax the structure?
> >
> >
> > > 2 - is there a "trick" to fixing what I have?
> > >
> >
> > There are lots of tricks. I would start with setting ncyc to a large
> value
> > and setting strong restraints on the 'known' coordinates, allowing only
> > those that swissPDB viewer added to relax.
> >
> >
> > >
> > >
> > >
> > > 3 - is there a better (easier) way to build out missing residues denovo
> > >
> > > (letting amber build them by leaving out the residues does not work as
> it
> > >
> > > fills in the missing atoms in a straight line - not in a loop as I
> need)
> > >
> >
> > The archives of this mailing list may have some useful tidbits (I recall
> > this type of thing being discussed before, but can't remember specifics).
> > I'm sure there are better alternatives, but I have no experience with
> them.
> >
> > Good luck,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 24 2013 - 11:00:02 PDT
