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
> >
> >
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> >
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Received on Tue Mar 22 2016 - 05:00:03 PDT
