You have to give more info about what you did and the exact error message
xleap gave. Improper torsions are parameters to keep a rings/functional
groups planar. If you have the correct library for your modified
nucleoside, the impose command should work without any problem.
Ilyas Yildirim, Ph.D.
---------------------------------------------------------------
= Hutchison Hall B#10 - Department of Chemistry =
= - University of Rochester =
= 585-275-6766 (office) - =
=
http://www.pas.rochester.edu/~yildirim/ =
---------------------------------------------------------------
On Sat, 12 Jun 2010, Navanath Kumbhar wrote:
> Dear Sir,
>
> Thank you for early reply.
>
> I have changed dihdral angle for modified nucleosides in sybyl7.3 and open
> this file in xleap, i also load prep and frcmod file for this nucleosides .
> when i want to save top and crd files it gives error as
>
> improper torsion parameter
>
> So please tell me how i can used modified nucleosides in xleap and how i
> saved prmtop and inpcrd files.
>
> Thanks and great regards
> from
> Navanath Kumbhar
>
> On Sat, Jun 12, 2010 at 4:46 PM, Ilyas Yildirim
> <yildirim.pas.rochester.edu>wrote:
>
>> Look at the 'impose' command in Leap. You can do any kind of manipulation
>> you want. In order to change a dihedral angle
>>
>> impose mol {1} { {A1 A2 A3 A4 X1}}
>>
>> where Ai (i=1 to 4) are the atom names and X1 is the dihedral angle you
>> want the A1-A2-A3-A4 torsion to be. 'mol' is is the name of the molecule
>> and {1} is the residue number.
>>
>> Ilyas Yildirim, Ph.D.
>> ---------------------------------------------------------------
>> = Hutchison Hall B#10 - Department of Chemistry =
>> = - University of Rochester =
>> = 585-275-6766 (office) - =
>> = http://www.pas.rochester.edu/~yildirim/<http://www.pas.rochester.edu/%7Eyildirim/> =
>> ---------------------------------------------------------------
>>
>> On Sat, 12 Jun 2010, Navanath Kumbhar wrote:
>>
>>> Dear Amber community,
>>>
>>> can i define torsion angle value in xleap?
>>>
>>> if will do please tell me how can i do this.
>>>
>>> Thanks and great regards
>>> from
>>> Navanath Kumbhar
>>> _______________________________________________
>>> 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
>>
> _______________________________________________
> 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 Sat Jun 12 2010 - 06:00:06 PDT
