As Carlos mentioned you're not using the correct format for restraint
input. I suggest trying the 'rst' command in cpptraj, which can help
generate namelist restraint input using Amber atom mask expressions,
which you may find easier to use. See the manual for full details.
-Dan
On Mon, Sep 11, 2017 at 1:21 AM, Nisha Amarnath Jonniya
<phd1601271002.iiti.ac.in> wrote:
> 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
>> >
>> >
>> _______________________________________________
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>>
>
>
>
> --
>
> 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
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Sep 11 2017 - 06:30:04 PDT
