Dear Dr. David,
Thank you for your response.
Actually, I want to build a polymer using a monomer. So, is this possible
to use "bond" command between two (.pdb) files?
Thank you again!
Sincerely,
Pinky
On Thu, Aug 27, 2020 at 7:10 AM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Aug 26, 2020, Pinky Mazumder wrote:
> >
> >I am trying to build a cross-linking polymer of lignin...
>
> >Could you please share if there are any other commands of generating PDB
> >files, please let me know.
> >
> >After that I need to load it in xleap to perform the simulation.
>
> Once you have a PDB file describing the coordinates of the system you want
> to
> simulate, there are two main ways of adding cross-links:
>
> 1. Put the information into CONECT records in the PDB file. LEaP will
> apply
> these (although it's always good to use ParmEd to check after you have the
> prmtop file). Some graphics programs might do this for you, or you can
> use a
> text editor to add them by hand.
>
> 2. Add "bond" commands to your LEaP script, describing the new bonds you
> want.
>
> (I don't think you can do both 1 and 2: do one or the other).
>
> ...hope this helps....dac
>
>
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--
Pinky, Sharmi
AL,US
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Received on Tue Nov 10 2020 - 19:30:02 PST
