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 - 04:30:03 PDT
