AMBER Archive (2009)

Subject: Re: [AMBER] Residues

From: KIRTANA S (skirtana4_at_gmail.com)
Date: Sat Jun 13 2009 - 19:14:31 CDT

I tried to connect my residues in xleap with below scripts and it worked
.But even after getting the w7.off file with all connectivity Here I have
attcahed my library file.
When I did check w7
I am getting message on missing parameters , and warning on close contact of
... angstrom between ....and .....
What does it imply .Please suggest .

Thanks and Regards
Kirtana

On Fri, Jun 12, 2009 at 11:36 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> 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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