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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Received on Mon Mar 21 2016 - 22:30:04 PDT
