Hi Mish,
I know how to use impose in xLeap but not in ptraj.
Based on your example,
if you want to change the angle Phi defined by 4 atoms, O6, C2, O3 and C3,
the command issued in xLeap is as follows:
impose mol {2 1} {{ O6 C2 O3 C3 30.0}}
This command changes the dihedral angle defined by the above four atoms to
30 degrees.
Hope this helps!
Sai
On Mon, Oct 24, 2011 at 4:49 AM, mish <smncbr.gmail.com> wrote:
> Dear all:
>
> I would like to ask about the use of "impose" command in ptraj. I have
> carbohydrates and initially I would like to generate their initial
> conformation by rotating them along the dihedral angle. Suppose, fallowing
> are the angle phi and psi:
> Phi :2.O6 :2.C2 :1.O3 :1.C3
> Psi :2.C2 :1.O3 :1.C3 :1.C4
>
> In order to write a command to rotate the attached residue by 30 degree, I
> tried :
> impose mol { 274 275 } { { O5 C1 O2 C2 0 } { O5 C1 O2 C2 30.0 } }
> impose mol { 274 275 } { { C1 O2 C2 C3 0 } { C1 O2 C2 C3 30.0 } }
>
> But this seems to change the co-ordinates by that particular vales. can you
> please write me how to use "impose" for such a task ?
>
> Sincerely
> Mish
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Received on Tue Oct 25 2011 - 08:30:03 PDT
