Re: [AMBER] Build long polymer from the monomer using Xleap

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Tue, 07 Apr 2015 07:52:51 +0200

Dear James,

> I need to build long polymer consisted of several monomers and make
> all input files for amber simulation. Here monomer is some
> non-standart residue for which I also have force field parameters (in
> amber-accept form) made by external software. I'd be very thankful if
> someone provide me with the suggestions how it could be done using
> xleap or alternatively another software.

You can find a tutorial about building polymers at q4md-forcefieldtools.org
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php

notions of head/tail and fragments:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#2

For peptides & proteins:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#25

For nucleic acids:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#27

Automatic procedures:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#26
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#28

This approach can be used for non-standard residues: R.E.D. & PyRED
are designed for that...

The mol3 file format has advantages for molecular fragments:
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php

regards, Francois



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Received on Mon Apr 06 2015 - 23:00:03 PDT