Kirtana,
> 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,
I do not understand what you mean by "preserve".
> since I find that
> after using the connectivity my overall structure defines each fragment as a
> residue.
Yes, this is way it has to be set up...
You could also use the savemol2 command as defined .
http://q4md-forcefieldtools.org/Tutorial/leap.php
> It is possible that I can preserve my residues as I require them to
> be.
Once again I do not undertsnad what you mean by "preserve".
> 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 .
This is normal
> So how
> should I go about for connectivity of my fragments.
Once the tail and the queue have been defined the number of times you
need, you can solvate your system (if required), add the ions (if
required) and then save the prmtop/prmcrd files.
regards, Francois
>> 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
>>>
>>
>>
>
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Mon Jul 06 2009 - 10:03:55 PDT
