Dear Jiomm,
> I am working on some polymeric system and want to introduce
> naphthalene like ring system in polymer at intervals. I am using
> sequence command to add ring residues to the polymer. As polymer is
> a complex system so when I add a ring residues at intervals of
> polymer using sequence command few rings are added in such a manner
> that some polymer fragments criss cross the ring. Its not a good
> idea to somehow relax the rings using xleap one by one as there are
> many ring systems.
let's take an example: the "NGLY ALA GLY ALA CGLY" oligomer; if you do
want to build a naphthalene like polymer, the idea is highly similar...
- You first have to define the head/tail in the FF libs; see for instance:
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
then you can use the 'sequence' command:
MOL = sequence {NGLY ALA GLY ALA CGLY}
the 'impose' command can help if it does what one wants ;-)
If you want to relax the whole oligomer (or a part of the oligomer),
you have to first load a force field (FF) and correctly define the FF
atom types:
See
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php#2
- another approach would be to first load an experimental structure to
the PDB file format & then the FF libs; LEaP will match the
conformation defined in the PDB file. Here you could also remove some
atoms from the PDB file and let LEaP add the missing atom(s) according
to the FF libs (for instance remove the side chains and keep the
backbone)
- obviously you can run a conformational search...
regards, Francois
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Received on Wed Feb 27 2013 - 01:30:03 PST
