Hi,
If possible could you send me (off-list) the parm and restart files
(tar.gz) if they are not too large? I haven't been able to reproduce
the behavior you are seeing using similar input. Thanks!
Also, you appear to be using DRMSD and RMSD interchangeably - note
that they can be similar but are fundamentally different measurements;
the former is the mean deviation of internal distances while the
latter is the mean coordinate deviation (with or without a best-fit
rotation depending on presence of the 'nofit' keyword).
-Dan
On Tue, Aug 14, 2012 at 12:57 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> Hello all,
>
> I just found out that Rg and RMSD analysis might be problematic using
> "cpptraj"
> if the *.inpcrd file is included.
> (When I tried "ptraj", Rg and RMSD was OK)
>
>
> I also found out that the problem is with the first "reimaging" step (
> step A) see below ).
>
> When I used "cpptraj" the molecular structure in some frames (that with
> -nan) was
> somewhere very far (I was able to read in the reimaged trajectory into
> Chimera,
> but was not able to focus molecular structure in that frames).
>
> When I used "ptraj" for reimaging, all frames in reimaged trajectory was
> OK and
> the consequent Rg, RMSD analysis of this trajectory with "cpptraj" was OK
> as well.
>
> So the problem is here clearly just with "reimage" step.
>
> Below are for illustration obtained "cpptraj results" for cases
> with/without *.inpcrd file as
> the first frame (here "cpptraj" was used for the whole procedure A)
> imaging and B) analysis).
>
>
> Best wishes,
>
> Marek
>
>
> RESULTS
>
> CASE WITH INPCRD file as the first frame
>
> Rg
>
> #Frame RoG_00000 Max_00001
> 1 21.1165 37.1483
> 2 -nan 0.0000
> 3 -nan 0.0000
> 4 -nan 0.0000
> 5 -nan 0.0000
> 6 -nan 0.0000
> 7 -nan 0.0000
> 8 -nan 0.0000
> 9 18.7367 35.8859
> 10 -nan 0.0000
> 11 19.1161 36.6846
> 12 -nan 0.0000
> 13 18.9645 32.3899
> 14 -nan 0.0000
> 15 18.8792 32.7650
> 16 -nan 0.0000
> 17 18.4168 37.4452
> 18 -nan 0.0000
> 19 -nan 0.0000
> 20 -nan 0.0000
> 21 -nan 0.0000
> 22 -nan 0.0000
> 23 19.0636 41.6257
> 24 -nan 0.0000
> 25 -nan 0.0000
> 26 -nan 0.0000
> 27 -nan 0.0000
> 28 -nan 0.0000
> 29 -nan 0.0000
> 30 -nan 0.0000
> 31 -nan 0.0000
> 32 -nan 0.0000
>
>
> RMSD
>
> #Frame DRMSD_00002
> 1 0.0000
> 2 -nan
> 3 -nan
> 4 -nan
> 5 -nan
> 6 -nan
> 7 -nan
> 8 -nan
> 9 7.7264
> 10 -nan
> 11 8.2911
> 12 -nan
> 13 8.4795
> 14 -nan
> 15 8.6235
> 16 -nan
> 17 9.0447
> 18 -nan
> 19 -nan
> 20 -nan
> 21 -nan
> 22 -nan
> 23 8.8635
> 24 -nan
> 25 -nan
> 26 -nan
> 27 -nan
> 28 -nan
> 29 -nan
> 30 -nan
> 31 -nan
> 32 -nan
>
>
>
> CASE WITHOUT INPCRD file as the first frame
>
> Rg
>
> #Frame RoG_00000 Max_00001
> 1 20.4278 36.8550
> 2 19.7771 38.6546
> 3 19.7454 37.6637
> 4 19.1045 39.5584
> 5 18.7786 39.3899
> 6 18.6147 37.2790
> 7 18.4753 33.0033
> 8 18.7367 35.8859
> 9 19.0431 36.5700
> 10 19.1161 36.6846
> 11 19.1758 35.7522
> 12 18.9645 32.3899
> 13 18.9658 34.4183
> 14 18.8792 32.7650
> 15 18.5999 38.0307
> 16 18.4168 37.4452
> 17 18.4572 39.1773
> 18 18.2946 39.6647
> 19 18.2647 41.3678
> 20 18.0115 40.0566
> 21 18.8405 39.8609
> 22 19.0636 41.6257
> 23 18.5178 40.4262
> 24 17.9904 33.7236
> 25 18.2254 33.1004
> 26 18.4423 36.5427
> 27 18.6103 40.3092
> 28 18.4138 39.1428
> 29 17.9545 37.3046
> 30 17.5413 37.2142
> 31 18.1139 39.8293
>
> RMSD
>
> #Frame DRMSD_00002
> 1 0.0000
> 2 3.7271
> 3 4.2589
> 4 5.0444
> 5 6.2434
> 6 6.3137
> 7 6.6319
> 8 6.1484
> 9 6.1097
> 10 6.6053
> 11 6.6902
> 12 7.1798
> 13 6.9626
> 14 7.4241
> 15 7.6087
> 16 7.9724
> 17 7.7480
> 18 7.9730
> 19 7.9310
> 20 8.1429
> 21 8.1940
> 22 7.8698
> 23 8.2837
> 24 8.2652
> 25 8.4545
> 26 8.1110
> 27 8.0963
> 28 8.1539
> 29 8.6305
> 30 8.7929
> 31 8.5637
>
>
>
>
> USED PROCEDURE
>
> A) - creation of reimaged trajectory "prod_REIMAGED_RST.mdcrd"
>
> trajin ../P-G3-PROTONATED15proc.inpcrd
> trajin ../prod_1.rst
> trajin ../prod_2.rst
> trajin ../prod_3.rst
> trajin ../prod_4.rst
> trajin ../prod_5.rst
> trajin ../prod_6.rst
> trajin ../prod_7.rst
> trajin ../prod_8.rst
> trajin ../prod_9.rst
> trajin ../prod_10.rst
> trajin ../prod_11.rst
> trajin ../prod_12.rst
> trajin ../prod_13.rst
> trajin ../prod_14.rst
> trajin ../prod_15.rst
> trajin ../prod_16.rst
> trajin ../prod_17.rst
> trajin ../prod_18.rst
> trajin ../prod_19.rst
> trajin ../prod_20.rst
> trajin ../prod_21.rst
> trajin ../prod_22.rst
> trajin ../prod_23.rst
> trajin ../prod_24.rst
> trajin ../prod_25.rst
> trajin ../prod_26.rst
> trajin ../prod_27.rst
> trajin ../prod_28.rst
> trajin ../prod_29.rst
> trajin ../prod_30.rst
> trajin ../prod_31.rst
>
> trajout prod_REIMAGED_RST.mdcrd netcdf
>
> center :1
> image familiar
>
>
>
> B) - Rg and RMSD analysis of reimaged frames
>
> trajin prod_REIMAGED_RST.mdcrd
>
> radgyr out DEN_RST.RGYR :CEN,REC,REP,REE,ENP,EN0
>
> drmsd :CEN,REC,REP,REE,ENP,EN0 first out DEN_RST.RMSD
>
> (rms first out DEN_RST.RMSD :CEN,REC,REP,REE,ENP,EN0 - in case of "ptraj")
>
>
>
>
>
>
>
>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
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> 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)
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Received on Tue Aug 14 2012 - 16:00:06 PDT
