I don't think you've yet done the testing to isolate the many variables
that you have introduced.
In a clean, empty directory you should build a duplex using only standard
force fields, nothing you have modified. Test this and see if the bases are
planar. If not, let us know, but that would not match my experience. If
they are planar, then in a different new, simply directory do the same with
your modified parameters. It must be a different directory so the leap log
has only 1 attempt to build in it. If you need to run leap again, delete
the log along with any output before to try again.
You need to determine if your modified parameters are the source of the
problem. Then you can investigate why. Modifying a force field is an
advanced topic and you should make sure you are already familiar with md
simulations and how to analyze your topology files before trying to change
the force field. Most likely you are changing the parameters for normal
bases in a way that is incorrect.
On Mar 30, 2016 11:13 PM, "Prayagraj Fandilolu" <fprayagraj.gmail.com>
wrote:
> Hi,
>
> I am new to Parmed and i have tried the printdihedrals from parmed...
>
> But i am not sure what torsions to check for??
>
> I am experiencing trouble in each residue's glycosyl and side chain
> nitrogens...
>
> When i put those nitrogens for printdihedrals, i get a huge list of
> torsions which can not be interpreted by me..
>
> Single residue and atom selection in printdihedrals gives a smaller output
> but the values given do not seem to be the torsion angle values....
>
> I am not getting what to do with these values???
>
> Sending herewith the frcmod file and a snapshot of parmed output..
>
> Kindly help me.
>
> Thanks in advance!!!
>
> Prayagraj Fandilolu
> Research Scholar,
> Structural Bioinformatics Unit
> Department of Biochemistry
> Shivaji University, Kolhapur - 416004
> (MS) India
>
> On Tue, Mar 22, 2016 at 5:00 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > I'm not sure if you saw the last reply by Dave Case on 3/2 - he gave you
> > some useful advice but it doesn't look like you have tried that yet.
> >
> >
> > On Tue, Mar 22, 2016 at 1:28 AM, Prayagraj Fandilolu <
> fprayagraj.gmail.com
> > >
> > wrote:
> >
> > > Hi David Sir,
> > >
> > > I took much time to reply to this mail. I did a cross check again for
> my
> > > inputs. I reconstructed the structure using SYBYL and Chimera
> softwares.
> > I
> > > tested and derived the parameters once again.
> > >
> > > As you have said, i prepared a test case in which i used an RNA duplex
> > > system in ff14SB. This test case is working fine no disposition form
> the
> > > structure was observed..
> > >
> > > But when i am using my systems i am getting the same problem again.
> > >
> > > I am using xleap in which my sequence of commands is like this:
> > >
> > > *Using ff14SB*
> > > source leaprc.ff14SB
> > > source leaprc.modrna08
> > > loadamberparams frcmod.ionsjc_tip3p
> > > loadamberprep PMF.prepin
> > > loadamberparams PMF.frcmod
> > > set PMF head PMF.1.P
> > > set PMF tail PMF.1.O3'
> > > asl=loadpdb asl.pdb
> > > check asl
> > > addions asl Na+ 0
> > > solvatebox asl TIP3PBOX 10
> > > saveamberparm asl asl.prmtop asl.inpcrd
> > >
> > > *Using older ff:*
> > > source leaprc.rna.ff99
> > > source leaprc.ff99bsc0
> > > source leaprc.modrna08
> > > loadamberparams frcmod.ol.dat
> > > loadamberprep PMF.prepin
> > > loadamberparams PMF.frcmod
> > > set PMF head PMF.1.P
> > > set PMF tail PMF.1.O3'
> > > asl=loadpdb asl.pdb
> > > check asl
> > > addions asl Na+ 0
> > > solvatebox asl TIP3PBOX 10
> > > saveamberparm asl asl.prmtop asl.inpcrd
> > >
> > > The leap log for both the cases absolutely show no error. But the
> > planarity
> > > is hampered in both cases. How can i check whether the prepin file is
> > > faulty or not? I have previously sent all the mentioned files.
> > >
> > > Kindly guide me in this issue......
> > >
> > > Thanks in advance..
> > >
> > > Prayagraj Fandilolu
> > > Research Scholar,
> > > Structural Bioinformatics Unit
> > > Department of Biochemistry
> > > Shivaji University, Kolhapur - 416004
> > > (MS) India
> > >
> > > On Wed, Mar 2, 2016 at 6:24 PM, David A Case <david.case.rutgers.edu>
> > > wrote:
> > >
> > > > On Wed, Mar 02, 2016, Prayagraj Fandilolu wrote:
> > > > >
> > > > >
> > > > > 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).
> > > >
> > > > I think what Carlos (and others reading this) want is simpler
> example:
> > do
> > > > you have a case (preferably with a *short* oligonucleotide) where you
> > get
> > > > non-planar nitrogens, and that involves only standard nucleotides and
> > no
> > > > additional changes or parameter files? We would need the leap.in
> file
> > > > that you used. (A good test case might involve just a single base.)
> > > >
> > > > The point is to find out if there is really a bug in ff14SB, or
> whether
> > > > the problems you report are arising from changes you are making,
> either
> > > > with modified nucleotides or with making changes to a prepin file.
> > > >
> > > > [Please note: on successive runs, tleap keeps adding to the end of
> the
> > > > leap.log file, so that you can get a file that contains information
> > > > about many separate tleap invocations. Please delete (or rename)
> your
> > > > "leap.log" file before running a test case. I find it almost
> > impossible
> > > > to understand the files you sent for this reason, or even to locate
> > what
> > > > you describe as "warnings about improper torsions". And the leap.in
> > file
> > > > is
> > > > generally more useful than the leap.log file, since the former makes
> it
> > > > easier
> > > > to see what is being done, and to try to reproduce the problem.]
> > > >
> > > > [Second note: if you can make a small test case, then the
> > > "printDihedrals"
> > > > command in parmed can be used to examine the torsion parameters in a
> > > given
> > > > prmtop file without having you be overwhelmed with output. Or, even
> > in a
> > > > bigger system, use "printDihedrals <mask>" can be used to focus
> > attention
> > > > on a
> > > > single base.]
> > > >
> > > > ...thanks...dac
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 31 2016 - 03:00:03 PDT
