Re: [AMBER] tLeap sequence overlap with new residues

From: David A Case <>
Date: Mon, 12 Nov 2018 08:18:50 -0500

On Sat, Nov 10, 2018, David Poole wrote:

>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.

Two points to note:

1. tleap is not generally a structure-building program. The most common
usage is for coordinates to be input (via a pdb file) from some other
source of information (x-ray structure, homology model, some other
program). The fact that a command like "sequence {ALA GLY ASP}" sort-of
works (by producing a completely extended chain) is probably specific to
the specific nature of the connection in amino acids.

2. That said, it might be possible to fix the problem you describe by
use of the impose command, which allows you to specify torsion angles
for the connections. But it's hard to understand exactly what is going
wrong from your description, and it could be that the mol2 file or
library file have some problems. Can you post the .lib file plus the
exact tleap commands you used?

>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.

Could be releated to that above, or could easily be a bug. I'm thinking
that very few people ever use the saveAmberPrep command (if that is indeed
what you did). Again, can you provide the files and commands that would
be needed to reproduce the problem?


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Received on Mon Nov 12 2018 - 05:30:02 PST
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