Hello Sir,
I am using PDB 1EHZ with all its modified bases. I am sourcing ff99bsc0
before sourcing leaprc.modrna08
I am using xleap from ambertools15.
To find out the problem I have tried the subsets of pdb and I found the
problem in 7MG residue. The dihedral missing is here in the residue..
For more details and command syntax I am attaching the .log file for your
reference.
I will be highly obliged if I could know what should be my next steps to
solve the issue??
Thanks in advance…
Prayagraj Fandilolu
Research Scholar,
Structural Bioinformatics Unit
Department of Biochemistry
Shivaji University, Kolhapur - 416004
(MS) India
On Mon, Apr 25, 2016 at 6:03 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Sun, Apr 24, 2016, Prayagraj Fandilolu wrote:
> >
> > **No torsion terms for CB-N*-CR-H5
> >
> > I am using parameters from leaprc.modrna08 with ff99bsc0.
>
> Please post the *exact* commands you gave to tleap. It would also help
> if you gave us the PDB id you are using. What version of amber? Are you
> following the instructions at the top of the leaprc.modrna08 file?
>
> Do you have modified RNA bases? If so, please try different subsets of
> the pdb file to see if the problem is related to the modified bases, or
> not. Trying to find a minimal PBB file that shows the error would be a
> good first step.
>
> ....dac
>
>
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- application/octet-stream attachment: trna3.log
Received on Wed Apr 27 2016 - 23:30:04 PDT
