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 - 01:30:03 PST
