AMBER Archive (2009)

Subject: Re: [AMBER] Residues

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jun 12 2009 - 10:36:10 CDT

Kirtana,

> Thanks for the documents I shall go through them .But is there any way to
> script for more than one tails in the mainchain.dat file .

The idea is the following:

You define the head of unit-1 & the tail of unit-2
You connect unit-1 + unit-2 as a new unit-3
You define the new head (or tail) of Unit-3
You connect Unit-3 with another Unit...
etc...

regards, Francois

>> Is it possible to connect the residues with multiple connectivity using
>>> xleap.I would like to know if I have multiple tails in each of my residue
>>> how should I use it in the mainchain.dat file and make the connectivity
>>> in
>>> xleap.I referred it from the tutorial
>>> http://ambermd.org/antechamber/dna.htm
>>>
>>
>> You might be interested in looking as well @
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26
>>
>> With the corresponding LEaP script defining tails and queues for branched
>> systems:
>> http://q4md-forcefieldtools.org/REDDB/projects/F-71/script1.ff
>> also available from
>> http://q4md-forcefieldtools.org/REDDB/projects/F-71/
>>
>> Another good example is also the CYX residue in the Amber force field
>> topology database:
>> xleap -f leaprc.ff99
>> desc CYX
>> desc CYX.1
>>
>> regards, Francois

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