Dear All,
I am trying to restraint pseudodihedral angle of RNA duplex while
running umbrella sampling.
Here I am attaching the DISANG.RST file for running minimization in
umbrella sampling.
I would like to use com (center of mass) notation for restraining these
pseudodiheral angle including 3 sugar and 1 base.
So, can anyone please help to figure out this com notation for restraining
these 3 sugar and 1 nitrogenous base.
What could be the code for this?
Following ERROR I am getting while running:
At line 1032 of file nmr_calls.F90 (unit = 33, file = 'disang2.rst')
Fortran runtime error: Bad data for namelist object iat
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
Herewith attaching the disang.rst file.
On Fri, Sep 8, 2017 at 8:50 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> this is not the correct format for the restraint input. I suggest looking
> at the manual in detail. It's hard to help more because I can't figure out
> exactly what you're trying to do. There should be a separate rst line for
> each of the restraints that you want to impose.
>
> On Fri, Sep 8, 2017 at 10:57 AM, Nisha Amarnath Jonniya <
> phd1601271002.iiti.ac.in> wrote:
>
> > Dear Sir,
> >
> > I am attaching the disang.rst file.
> > In this file, first 5 atoms for for sugar of 15th residues,
> > next 5 for sugar of 4th , then next 5 sugar of 6th residues and last all
> > atoms of bases of 5th residues.
> > This kind of restraint I want.
> > Only error is of peudidihedral angle , for chi values it is not showing
> any
> > error.
> >
> >
> >
> > On Fri, Sep 8, 2017 at 6:20 PM, <diego.soler.uam.es> wrote:
> >
> > > Dear Nisha,
> > >
> > > I'd recommend you to share your scripts in detail so we can try to
> > > spot some bugs.
> > >
> > > Best,
> > > Diego SP
> > >
> > >
> > > Quoting Nisha Amarnath Jonniya <phd1601271002.iiti.ac.in>:
> > >
> > > > Dear All,
> > > >
> > > > I am new to umbrella sampling.
> > > > here, I would like to do umbrella sampling of RNA duplex with
> > > > pseudodihedral angle and chi (torsion) angle restraint.
> > > >
> > > > In disang.rst file
> > > > &rst iat= 463,482........138
> > > >
> > > > with r1,r2,r3,r4 and rk2 and rk3 values.
> > > >
> > > > iat contains in total 25 atoms corresponding to sugar atoms of 15th,
> > > > 4th,6th residues and base atoms of 5th residues, so in total 25
> atoms
> > > to
> > > > restraint pseudodihedral angle.
> > > >
> > > > Only error is coming while incorporating theta value i.e
> pseudodihedral
> > > > angle and that too after 102... and not before that.
> > > >
> > > > while running these file , it's showing error
> > > >
> > > >
> > > > *Following ERROR I am getting while running disang1.rst :*
> > > >
> > > > *At line 1032 of file nmr_calls.F90 (unit = 33, file =
> 'disang1.rst')*
> > > >
> > > >
> > > >
> > > >
> > > > *Fortran runtime error: Cannot match namelist object name
> > > > 102104170189187167169145147148151152142143144141139138------
> > > -------------------------------------------------Primary
> > > > job terminated normally, but 1 process returneda non-zero exit
> code..
> > > Per
> > > > user-direction, the job has been aborted.*
> > > >
> > > >
> > > >
> > > > Please suggest me what to do.
> > > >
> > > >
> > > >
> > > > --
> > > >
> > > > Nisha Amarnath Jonniya
> > > > PhD Research Scholar
> > > > Biosciences and Biomedical Engineering
> > > > Indian Institute of Technology, Indore
> > > > India
> > > > _______________________________________________
> > > > 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
> > >
> >
> >
> >
> > --
> >
> > Nisha Amarnath Jonniya
> > PhD Research Scholar
> > Biosciences and Biomedical Engineering
> > Indian Institute of Technology, Indore
> > India
> >
> > _______________________________________________
> > 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
>
--
Nisha Amarnath Jonniya
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Sep 10 2017 - 22:30:02 PDT
