Hi,
On Thu, Dec 26, 2013 at 4:03 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> I have 1 microsecond trajectory and each frame is saved every 10 ps. I
> m using following command to perform clustering analysis
>
> trajin prod1.mdcrd 1 1000 1
> trajin prodX.mdcrd 1 1000 1
>
FYI, if your trajectory is 1 microsecond saved every 10 ps you should have
100,000 frames total. Here you are only using the first 1000 frames from
prod1.mdcrd and prodX.mdcrd. If you just want to read in all frames from a
trajectory you don't need any of the start, stop, or offset arguments.
> strip :WAT
> strip :Cl-
> strip :Na+
>
These can be combined into 1 command, "strip :WAT,Cl-,Na+"
> cluster hieragglo epsilon 4 averagelinkage rms.CA sieve 10 out
> cnumvtime summary summaryfile clusterout clus clusterfmt amber repout
> repclus repfmt pdb
>
> I get following warning:
> Warning: [cluster] Not all arguments handled: [ sieve 10 ]
>
I suspect you're using an out-of-date version of cpptraj (12.X or less).
Please update to the latest version from AmberTools 13.
-Dan
--
-------------------------
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) 585-6208 (Fax)
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Received on Thu Dec 26 2013 - 07:00:04 PST
