Sir,
Thank you for your constant support and help..
I am still trying to solve the problem..
As you've said, I took a careful look into the leap outputs and tried to
correct them with my original system.
Today i tried loading two systems successively in two sessions.
The warnings about improper torsion (old.log) were treated by adding an
additional improper into the prepin file (new.log).
This eliminated the warnings from leap output but the problem with
planarity still persists.
Sir, I know i might me disturbing you a lot.. but kindly tell me is there
any tools or protocol by which i can check my input structure for such
issues with hybridization or atom types?
I am herewith sending the two logs from leap...
Kindly take a look......
Thanking you,
Mr. Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
On Wed, Mar 2, 2016 at 6:19 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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- application/octet-stream attachment: New.log
- application/octet-stream attachment: old.log
Received on Wed Mar 02 2016 - 02:00:04 PST
