Dan or Tom would probably know this better than me, but it seems that the
existence of spaces in the mask definition (without using "" to encompass
them) could be problematic, as the parser would interpret that as different
tokens. No guarantee this is true, since I'm not a ptraj expert.
Do you get the same answer if you either put quotes around the mask or get
rid of the spaces?
Good luck,
Jason
On Wed, Mar 23, 2011 at 4:50 PM, Chris Chris <alpharecept.yahoo.com> wrote:
> I used ptraj with the following input file:
>
>
> trajin g1tetra_prod_mdx1
> trajin g1tetra_prod_mdx2
> rms first out g1tetra_rms_1_112.dat :1-112 .CA, C, N
> strip :WAT
> go
>
>
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Wed, March 23, 2011 6:15:58 PM
> Subject: Re: [AMBER] odd output from rms measurement
>
> We need to know how this was calculated.
>
> On Mar 23, 2011 5:56 PM, "Chris Chris" <alpharecept.yahoo.com> wrote:
>
> Can someone help me explain the attached graph? Basically, I'm simulating
> binding energies of a group of artificial peptides. I replaced the side
> chains
> of tropomyosin with the side chains of my peptides. I'm doing long
> production
> simulations so that the structure can 'acclimate' to my grafting of the new
> side
> chains
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 23 2011 - 18:00:02 PDT
