[AMBER] tLeap sequence overlap with new residues

From: David Poole <thepoole.ucdavis.edu>
Date: Sat, 10 Nov 2018 15:45:13 +0100

I had read somewhere in the documentation that tleap can be used for more
than biopolymers, since I had a project with abiological polymers, I
decided to try it out on some simple polystyrene.

Following usual methods I produced a mol2 file and frcmod file for a
monomer unit, and then defined the connect0/head and connect1/tail atoms in
a new library, and this works well. But alas, when I use the sequence
command to make a series of monomers, all the 'side chain' groups are
overlaid whereas only the head and tail atoms are placed in sequence.

I also noticed when I tried to save an amber prep file of the unit, it only
saved the head/tail carbons and the 3 hydrogens adjacent, but nothing else.
This might be related, but I am not sure.

Thanks for your help,
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Received on Sat Nov 10 2018 - 07:00:03 PST
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