Dear Amber users,
I did the connectivity with the process as you had replied in the previous
> mail.How can I preserve my residues as it is originally , since I find that
> after using the connectivity my overall structure defines each fragment as a
> residue .It is possible that I can preserve my residues as I require them to
> be.
I had used the following
set q1 tail q1.1.atom name
I had made the connections by defining a new tail each time and make the
connectivity .In my pdb file obtained after minimization from the topology
and coordinate files has TER cards separating each of fragment . So how
should I go about for connectivity of my fragments.
>
> I appreciate your help in this regard.
>
> Thanks and Regards
> Kirtana
>
>
> On Fri, Jun 12, 2009 at 11:36 AM, FyD <fyd.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
>>>>
>>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 06 2009 - 10:03:43 PDT
