That worked! Thank you!
Sent from my iPhone
On Mar 9, 2013, at 9:51 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This seems like an imaging issue. Did you try to re-image your
> trajectory at all? I recommend using the 'autoimage' command from
> AmberTools 12 cpptraj to image your trajectory prior to running your
> RMSD calculation.
>
> -Dan
>
> On Sat, Mar 9, 2013 at 6:55 PM, Kira Armacost
> <kza0004.tigermail.auburn.edu> wrote:
>> I have performed an RMSD calculation on a few 300ns trajectories and noticed that the RMSD plots didn't look right. I had spikes from 5 Angstroms to 11 Angstroms, one frame apart, so I pulled the pdb's from those frames and noticed that the ligand was not in the active site of the enzyme for that frame. I checked a few pdb's and only a few of them do that. On these trajectories I have also performed other calculations in ptraj (distance - including ones with the ligand, clustering and hydrogen bond) and only have this error when I perform RMSD. Here's my input script:
>>
>> trajin xx.crd.gz
>> rms first out rmsd.out time 0.01 :1-362
>>
>> I have noticed this problem before when I stripped the water from the enzyme for analysis, but in this case, the water is still there.
>>
>> Thanks!
>>
>> Kira A. Armacost
>> Ph.D Candidate
>> Department of Chemistry and Biochemistry
>> Auburn University
>> Dr. Orlando Acevedo Research Group
>> Concepts of Science GTA
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> 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 Mar 11 2013 - 07:30:03 PDT
