Dead Paragray,to preserve nitrate ions planarity in Gaff I use an
additional improper dihedral.You can think of something similar.Best
Lorenzo G.
Il 27/Feb/2016 10:08, "Prayagraj Fandilolu" <fprayagraj.gmail.com> ha
scritto:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat Feb 27 2016 - 01:30:04 PST
