I have only looked briefly at your leap outputs, but I see many problems
listed in the log files. Have you read through them carefully yet? Missing
files, new atoms created that were not in the templates and so on. I
haven't been able to look enough to determine the cause, but I can confirm
that our simulations of RNA with ff14SB, back and chiOL3 do not have the
planarity issue apparent in your structures. I suggest looking at the error
messages and seeing if you can fix the problems they describe.
On Mar 1, 2016 12:37 AM, "Prayagraj Fandilolu" <fprayagraj.gmail.com> wrote:
> Hello Sir,
>
> I am herewith sending the zip files of systems run under each of the two
> force fields.
>
> Thanking you,
>
>
> Mr. Prayagraj Fandilolu
> Research Scholar,
> Structural Bioinformatics Unit
> Department of Biochemistry
> Shivaji University, Kolhapur - 416004
> (MS) India
>
> On Sun, Feb 28, 2016 at 7:50 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > can you send me the leap input script for each, and the prmtop that leap
> > made for each?
> >
> > On Sun, Feb 28, 2016 at 2:53 AM, Prayagraj Fandilolu <
> fprayagraj.gmail.com
> > >
> > wrote:
> >
> > > Hi Carlos Sir,
> > >
> > > Sorry for late on my part..
> > >
> > > as you've said i tried all the parameters to find out what exactly is
> > going
> > > wrong with nitrogen....
> > >
> > > you got it correct when i load a normal RNA with ff14SB without my
> > > parameters and no frcmod i am experiencing the problem. And the same
> > system
> > > works fine with ff99bsc0...
> > >
> > > I am herewith sending the minimized pdbs for your reference...
> > >
> > > Kindly guide me in this case.....
> > >
> > > Thanking you in advance.....
> > >
> > > Prayagraj Fandilolu
> > > Research Scholar,
> > > Structural Bioinformatics Unit
> > > Department of Biochemistry
> > > Shivaji University, Kolhapur - 416004
> > > (MS) India
> > >
> > > On Sat, Feb 27, 2016 at 6:47 PM, Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > I'm sorry but this still isn't clear to me. you have many variables
> in
> > > your
> > > > protocol and you need to work on isolating them to determine which
> > factor
> > > > is the cause. for example, you load many force field variations, and
> > you
> > > > also have your own prepin and frcmod. you need to have very clear
> "this
> > > > works, this does not" where you have changed only 1 aspect of your
> > > > protocol.
> > > >
> > > > are you saying that when you load a normal RNA with ff14SB and none
> of
> > > your
> > > > modified parameters, no frcmod, that you have problems with
> planarity?
> > > and
> > > > the same thing but with ff99bsc0 works fine? ff14SB did not change
> RNA
> > > > parameters, so that would be unexpected.
> > > >
> > > > On Sat, Feb 27, 2016 at 8:00 AM, Prayagraj Fandilolu <
> > > fprayagraj.gmail.com
> > > > >
> > > > wrote:
> > > >
> > > > > Hello Carlos Sir,
> > > > >
> > > > > Thank you for your quick response.
> > > > >
> > > > > After a lot of trials and errors i also have reached on the same
> > > > > conclusion. As you said all other standard bases are also showing
> the
> > > > > planarity problem when i load the created prepin file.
> > > > >
> > > > > But the other system consisting of only the standard bases works
> fine
> > > in
> > > > > ff99bsc0 and rna.ff99. But the same system (Unmodified one)
> > experiences
> > > > the
> > > > > planarity issue when it is simulated using ff14SB.
> > > > >
> > > > > I would like to clear that i am not loading any prepared parameter
> > file
> > > > for
> > > > > unmodified system.
> > > > >
> > > > > Regarding creation of prepin file; i derived the parameters from
> > > > > antechamber using a PDB----->mol2------>prepin with bcc charges and
> > > amber
> > > > > atom types with net charge -1.
> > > > >
> > > > > I am uploading the derived prepin file for your reference. Kindly
> > find
> > > > the
> > > > > attachment.
> > > > >
> > > > > Thanking you.
> > > > >
> > > > > Mr. Prayagraj Fandilolu
> > > > > Research Scholar,
> > > > > Structural Bioinformatics Unit
> > > > > Department of Biochemistry
> > > > > Shivaji University, Kolhapur - 416004
> > > > > (MS) India
> > > > >
> > > > > On Sat, Feb 27, 2016 at 6:04 PM, Carlos Simmerling <
> > > > > carlos.simmerling.gmail.com> wrote:
> > > > >
> > > > > > I suspect that it isn't the ff14SB or other parameters that you
> are
> > > > > > loading, but probably is something to do with the new parameters
> > you
> > > > > > created for the modified base. One way to check this : do you
> have
> > > > > > non-planar problems for standard bases too? even when you do not
> > > load a
> > > > > > system with modified bases and new parameters? if it is your
> > > > parameters,
> > > > > > then you would need so share details about your prepin file and
> how
> > > you
> > > > > > generated any new parameters.
> > > > > >
> > > > > > On Sat, Feb 27, 2016 at 4:07 AM, Prayagraj Fandilolu <
> > > > > fprayagraj.gmail.com
> > > > > > >
> > > > > > wrote:
> > > > > >
> > > > > > > Dear all,
> > > > > > >
> > > > > > > I am again reporting a problem which I had previously discussed
> > > > here. I
> > > > > > > have done whatever I could, as per the suggestions of Mr. Jason
> > and
> > > > Mr.
> > > > > > > Carlos. I have not yet got the solution to the problem. Here I
> am
> > > > > sending
> > > > > > > the error details again…
> > > > > > >
> > > > > > > I am trying to simulate a tRNA system with few modified
> > > nucleosides.
> > > > I
> > > > > > have
> > > > > > > generated the parameters for a synthetic nucleoside which was
> not
> > > > > > available
> > > > > > > in leaprc.modrna08
> > > > > > >
> > > > > > > Everything goes fine till I put the system for minimization. In
> > > > sander
> > > > > > > output of minimization, I found that all the nitrogen atoms
> (with
> > > > three
> > > > > > > bonding atoms) lose their planarity and this is affecting the
> > > proper
> > > > > > atomic
> > > > > > > interactions and base stacking as well.
> > > > > > >
> > > > > > > I tried many other systems but the problem persists with them
> > too.
> > > > > > >
> > > > > > > I guess there is something conflicting within the force
> fields. I
> > > > have
> > > > > > > tried leaprc.rna.ff99 & leaprc.ff99bsc0 in combination and
> > > > individually
> > > > > > > also. Other force fields like ff14SB, ff12SB were also used
> > > > > individually
> > > > > > > but the problem persists.
> > > > > > >
> > > > > > > For each of the above force fields, I am using following
> commands
> > > in
> > > > > > leap:
> > > > > > >
> > > > > > > >>> source leaprc.abcforcefield
> > > > > > >
> > > > > > > >>> source leaprc.modrna08
> > > > > > >
> > > > > > > >>> loadamberparams frcmod.ol.dat (only for rna.ff99 and
> > ff99bsc0)
> > > > > > >
> > > > > > > >>> loadamberprep abc.prepin
> > > > > > >
> > > > > > > >>> loadamberparams abc.frcmod
> > > > > > >
> > > > > > > >>> pmf=loadpdb pmf.pdb
> > > > > > >
> > > > > > > >>> solvatebox pmf TIP3PBOX 8
> > > > > > >
> > > > > > > >>> addions pmf Na+ 0
> > > > > > >
> > > > > > > >>> saveamberparm pmf pmf.prmtop pmf.inpcrd
> > > > > > >
> > > > > > > The topology and coordinate files are generated successfully
> but
> > > when
> > > > > the
> > > > > > > system is subjected to minimization for 10,000 steps of SD, all
> > > > > nitrogen
> > > > > > > atoms of the system lose their planarity.
> > > > > > >
> > > > > > > Can someone help me getting into the solution of this error?
> > > > > > >
> > > > > > > Thanks in advance……….
> > > > > > >
> > > > > > > Prayagraj Fandilolu
> > > > > > > Research Scholar,
> > > > > > > Structural Bioinformatics Unit
> > > > > > > Department of Biochemistry
> > > > > > > Shivaji University, Kolhapur - 416004
> > > > > > > (MS) India
> > > > > > >
> > > > > > > On Tue, Feb 2, 2016 at 5:43 PM, Jason Swails <
> > > jason.swails.gmail.com
> > > > >
> > > > > > > wrote:
> > > > > > >
> > > > > > > > On Mon, Feb 1, 2016 at 11:15 PM, Prayagraj Fandilolu <
> > > > > > > fprayagraj.gmail.com
> > > > > > > > >
> > > > > > > > wrote:
> > > > > > > >
> > > > > > > > > Dear Amber users,
> > > > > > > > >
> > > > > > > > > I am simulating a RNA system using the ff14SB in Sander. I
> am
> > > > > facing
> > > > > > an
> > > > > > > > > issue with SP3 planar nitrogen atoms of my system. After
> > > > > > minimization,
> > > > > > > > the
> > > > > > > > > orientation of planar SP3 Nitrogen is changing and its
> planar
> > > > > > > > conformation
> > > > > > > > > is lost.
> > > > > > > > >
> > > > > > > > > I have checked the same system with older ff99bsc0. This ff
> > > works
> > > > > > fine
> > > > > > > > and
> > > > > > > > > the SP3 planar nitrogen atoms are still planar after
> > > > minimization.
> > > > > > > > >
> > > > > > > > > I am not getting a clue into this...
> > > > > > > > >
> > > > > > > > > can some one give me a solution to this issue????
> > > > > > > > >
> > > > > > > > > Other parameters being loaded with ff14SB are:
> > > > > > > > >
> > > > > > > > > frcmod.modrna08
> > > > > > > > > frcmod.chiOL4
> > > > > > > > >
> > > > > > > >
> > > > > > > > I'm not sure why you are loading these. The manual
> describes
> > > what
> > > > > > force
> > > > > > > > field each leaprc contains. Since you seem to be (??)
> loading
> > > > extra
> > > > > > > > parameters aside from what is loaded inside each leaprc
> itself,
> > > you
> > > > > are
> > > > > > > > *not* actually using ff14SB here.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > > frcmod.ionsjc_tip3p
> > > > > > > > >
> > > > > > > >
> > > > > > > > Loading ion parameters is necessary, as you've done here.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > >
> > > > > > > > > while in case of ff99bsc0 i am using:
> > > > > > > > >
> > > > > > > > > leaprc.rna.ff99
> > > > > > > > > leaprc.ff99bsc0
> > > > > > > > > frcmod.ol.dat
> > > > > > > > >
> > > > > > > >
> > > > > > > > Same comments above. leaprc.ff99bsc0 (now located in
> > > > > > > > oldff/leaprc.ff99bsc0) is the full specification of that
> force
> > > > field.
> > > > > > > >
> > > > > > > > The "extra" parameters you loaded may have been overwriting
> > > "good"
> > > > > > > > parameters with bad ones.
> > > > > > > >
> > > > > > > > HTH,
> > > > > > > > Jason
> > > > > > > >
> > > > > > > > --
> > > > > > > > Jason M. Swails
> > > > > > > > BioMaPS,
> > > > > > > > Rutgers University
> > > > > > > > Postdoctoral Researcher
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Received on Tue Mar 01 2016 - 17:00:03 PST
