> I would also like to know whether it is possible with ptrajin
> Below is the ptrajin script I used for finding the average for the 14mer.
>
> ****************************
> /disk1/people/programs/amber6/exe/ptraj bdna25leap_s.top << EOF
> trajin b25leapall1.strip.Z
> trajin b25leapall2.strip.Z
> average b25leapave_c10_2ns.pdb :1-28 pdb
> go
> EOF
Prior to calculating the average structure, you likely will want to image
the trajectory to put the strands together (in case they have
separated) and also RMS fit the conformations to a common reference
frame. Since you want the central 10 base pairs, likely you will want to
RMS fit to the central 10 base pairs prior to performing the
"average" since this is not done implicitly...
trajin b25leapall1.strip.Z
trajin b25leapall2.strip.Z
center :1-14 mass origin
image origin center
center :1-28 mass origin
image origin center
rms first mass out rms_to_central10.dat :3-12,17-26
average b25leapave_c10_2ns.pdb pdb :1-28
average b25leapave_c10only_2ns.pdb pdb :3-12,17-26
go
The second "average" will only dump out the central 10 base pairs.
Thomas E. Cheatham, III
Department of Medicinal Chemistry & Center for High Performance Computing
University of Utah INSCC 418
30 South 2000 East, Room 201 155 South 1452 East
Salt Lake City, Utah 84112-5820 Salt Lake City, Utah 84112-0190
cheatham_at_chpc.utah.edu
FAX: (801) 585-9119 FAX: (801) 585-5366
phone: (801) 587-9652 http://hnu.pharm.utah.edu/medchem/cheatham
Received on Fri Nov 03 2000 - 08:54:19 PST
