AMBER Archive (2009)

Subject: Re: [AMBER] Residues

From: KIRTANA S (skirtana4_at_gmail.com)
Date: Fri Jun 12 2009 - 10:07:50 CDT

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 .

Regards
Kirtana

On Fri, Jun 12, 2009 at 10:24 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> Dear Kirtana,
>
> 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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