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

From: James Starlight <jmsstarlight.gmail.com>
Date: Fri, 10 Apr 2015 13:40:12 +0200

Hi guys!

Simply I've made parametrization of the capped (2 CH3- connected to C
of the non-standard unit) monomer using ante-chamber, import its
params within my tleap script and tried to use SEQUENCE command to
build polymer but it didn't work. What I did wrong and how to fix it?


Thanks!!

J.

2015-04-07 7:52 GMT+02:00 FyD <fyd.q4md-forcefieldtools.org>:
> 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 Fri Apr 10 2015 - 05:30:02 PDT