Re: [AMBER] Help for building cross linking polymer using graphic antechamber

From: David A Case <>
Date: Thu, 27 Aug 2020 08:10:01 -0400

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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Received on Thu Aug 27 2020 - 05:30:02 PDT
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