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 Sat Feb 27 2016 - 05:30:07 PST
