AMBER Archive (2004)

Subject: Re: AMBER: RMSD calculations in ptraj and Carnal

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Tue Jun 15 2004 - 19:19:53 CDT

Hi,

I have detected the kind of behaviour, althought I might be using old
versions of both programs, carnal from amber6 and ptraj 6.5. Here is
some results:
  Frame Carnal Ptraj
  1 0.000000 0.00000
  2 1.211051 1.19757
  3 1.814778 1.46600
  4 2.327616 1.81870
  5 2.297854 1.59578
  6 2.993427 1.82320
  7 3.357107 1.96898
  8 3.714356 1.99161
  9 3.779510 2.24544
10 3.700370 2.13506
11 3.754412 2.59625
12 3.897156 2.59291
13 4.402024 2.53415
14 4.673463 2.68510
15 4.459503 2.96118
16 4.247532 2.84517
17 4.127878 2.72704
18 4.298431 2.77935
19 4.133379 2.72459
20 4.240111 2.69426
21 4.739150 2.74994
22 4.365342 2.77538
23 4.516887 2.90303
24 4.943164 2.94459
25 5.520181 2.96460
26 5.538829 3.05837
27 5.419526 3.03359
28 5.846064 3.17181
29 6.129072 3.03315
30 6.454406 2.91856
31 7.012384 3.00430
32 7.412052 3.07234
33 7.644817 3.21965
34 8.426695 3.45449

And this are the options used:
Ptraj:
trajin md06.crd
rms first out test.ptraj.rms :1-118 nofit
go

Carnal:
FILES_IN
         PARM p2 MODEL/pcaf2.top;
         STREAM s0 p2 md06.crd;
FILES_OUT
         TABLE rms test.carnal.rms;
DECLARE
         GROUP brd s0 (RES 1-118);
         RMS rms_brd brd;
OUTPUT
         TABLE rms rms_brd;
END

Bill Ross said the following on 06/15/04 16:55:
>>The trajectories are fitted, beafuase I keep the protein and part pof the
>>peptide fixed - basically 90% of the structure - so there is no CM
>>displacement.
>
>
> (or rotation, one would expect) - you are using the belly option
> I presume.
>
>
>>The way I discovered something was fishy was that I looked at a structure
>>in which all but one CA were 2Ang and more away from the reference
>>structure (up to 7Ang), yet ptraj listed an rmsd of less than 1Ang.
>
>
> I'd send ptraj input; maybe it was fitting?
>
>
>>When I
>>calculated by hand I got a figure of about 4Ang, which was more inline
>>with what I was observing visually.
>
>
> What did carnal give?
>
> Bill
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-- 
Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021

Tel: (212) 746-6375
Fax: (212) 746-6361
lug2002_at_med.cornell.edu

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