Hi Dan,
Dne Wed, 15 Aug 2012 00:30:33 +0200 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> 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!
OK, I will do it now.
>
> Also, you appear to be using DRMSD and RMSD interchangeably - note
Yes I know the difference but with DRMSD I had problem in case of PTRAJ
---------------------------------------------------------------------
PTRAJ: drmsd :CEN,REC,REP,REE,ENP,EN0 first out DEN_RST.RMSD.RMSD
WARNING in dispatchToken: Token string "drmsd" not found in tokenlist
----------------------------------------------------------------------
so just for the case of PTRAJ I used RMSD instead DRMSD (maybe DRMSD
is not implemented in PTRAJ but only in CPPTRAJ ?)
Best wishes,
Marek
> 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")
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
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>> http://www.opera.com/mail/
>>
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>
>
>
--
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Received on Wed Aug 15 2012 - 03:30:03 PDT
