Hi Karolina and Hannes,
Thank you very much for your suggestions.
I can now view them as distinct structures in VMD.
Regards
Sowmya
________________________________________
From: Karolina Mitusińska (Markowska) [markowska.kar.gmail.com]
Sent: Friday, June 02, 2017 1:25 PM
To: AMBER Mailing List
Subject: Re: [AMBER] TI MD simulation
Hi, Sowmya
I would suggest you to open your prepared structure (using both the .rst7
and .parm7 files) in VMD.
PyMOL does not always give the proper information about bonds.
Have a nice day,
Karolina Mitusińska
PhD student
2017-06-02 13:14 GMT+02:00 Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>:
> On Fri, 2 Jun 2017 10:57:33 +0000
> Sowmya Indrakumar <soemya.kemi.dtu.dk> wrote:
>
> > cpptraj -p *.parm7
> > >trajin *.nc 100 100 1
> > >strip :WAT,Cl-
> > >trajout *.pdb pdb
> > >run
>
> With this approach you will need to adjust the strip mask corresponding
> to your respective states, eg. "!:1-40" and "!:1-3,5-29,31-42"
>
>
> > Please see the attached image for reference. Coloured in yellow is
> > suppose to be bonded (-SS-) and the one in red is unbonded (-SH SH-).
> > while preparing the input files for simulation I have specifically
> > mentioned 'bond mol.4.SG mol.30.SG'. I still see it unbonded (marked
> > in yellow).
>
> I see a screenshot apparently from pymol. How do you inform pymol
> about bonds?
>
> Leap should give you feedback when the "bond" command fails. For
> visualisation you need to use a program/method that reads the
> information from the topology file so that you can actually check that
> it contains the wanted bonds.
>
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Received on Fri Jun 02 2017 - 05:30:03 PDT
