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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Received on Tue Aug 14 2012 - 12:30:05 PDT
