[gmx-users] DSSP problem
Mass
masstransfer_2010 at yahoo.com
Mon Oct 14 05:56:11 CEST 2013
Hi Justin
Here is the copied and pasted output
Mass at Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$
ls -l
total 92332632
-rw-rw-r-- 1 Mass Mass 0 Sep
8 19:46 310Helix.dat
-rw------- 1 Mass Mass 371878 Aug
21 07:39 3BLG_115XrayWater.top
-rw-rw-r-- 1 Mass Mass 282249 Sep
8 19:46 aHelix.dat
-rw-rw-r-- 1 Mass Mass 12963 Sep
9 20:00 average.pdb
-rw-rw-r-- 1 Mass Mass 12962 Aug
22 21:49 #average.pdb.1#
-rw-rw-r-- 1 Mass Mass 12963 Sep
1 20:18 #average.pdb.2#
-rw-rw-r-- 1 Mass Mass 39371 Aug
23 10:50 bLac_orig_md2-3_atomic-sas.xvg
-rw-rw-r-- 1 Mass Mass 1180585 Aug
22 22:20 bLac_orig_md2-3_radius-of-gyration.xvg
-rw-rw-r-- 1 Mass Mass 6151 Aug
23 10:50 bLac_orig_md2-3_residue-sas.xvg
-rw-rw-r-- 1 Mass Mass 538412 Aug
22 20:15 bLac_orig_md2-3_rmsd-Calpha-vs-start.xvg
-rw-rw-r-- 1 Mass Mass 2791 Aug
22 21:49 bLac_orig_md2-3_rmsf-per-residue.xvg
-rw-rw-r-- 1 Mass Mass 6739262 Aug
23 13:33 bLac_orig_md2-3_SecStruc.dat
-rw-rw-r-- 1 Mass Mass 1180736 Aug
23 10:50
bLac_orig_md2-3_solvent-accessible-surface.xvg
-rw-rw-r-- 1 Mass Mass 815104 Aug
23 10:32 #bLac_orig_md2-3_solvent-accessible-surface.xvg.1#
-rw-rw-r-- 1 Mass Mass 4696839648 Aug
22 15:58 bLac_orig_md2-3.xtc
-rw------- 1 Mass Mass 1539720 Aug
21 06:31 bLac_orig_md2.cpt
-rw------- 1 Mass Mass 7561608 Aug
21 06:31 bLac_orig_md2.edr
-rw------- 1 Mass Mass 4412810 Aug
21 06:31 bLac_orig_md2.gro
-rw------- 1 Mass Mass 7213156 Aug
21 07:39 bLac_orig_md2.log
-rw------- 1 Mass Mass 1539720 Aug
21 06:31 bLac_orig_md2_prev.cpt
-rw------- 1 Mass Mass 2075808 Aug
21 07:39 bLac_orig_md2.tpr
-rw------- 1 Mass Mass 15351454992 Aug
21 07:51 bLac_orig_md2.trr
-rw------- 1 Mass Mass 2348494832 Aug
21 06:41 bLac_orig_md2.xtc
-rw-rw-r-- 1 Mass Mass 7045242668 Sep
1 18:41 bLac_orig_md3-4.xtc
-rw------- 1 Mass Mass 1539720 Aug
21 06:19 bLac_orig_md3.cpt
-rw------- 1 Mass Mass 7561608 Aug
21 06:19 bLac_orig_md3.edr
-rw------- 1 Mass Mass 4412810 Aug
21 06:19 bLac_orig_md3.gro
-rw------- 1 Mass Mass 7212876 Aug
21 06:31 bLac_orig_md3.log
-rw------- 1 Mass Mass 1539720 Aug
21 06:19 bLac_orig_md3_prev.cpt
-rw------- 1 Mass Mass 2075808 Aug
21 06:31 bLac_orig_md3.tpr
-rw------- 1 Mass Mass 15351454992 Aug
21 07:39 bLac_orig_md3.trr
-rw------- 1 Mass Mass 2348579612 Aug
21 06:31 bLac_orig_md3.xtc
-rw-rw-r-- 1 Mass Mass 39519 Sep
9 20:54 bLac_orig_md4-5_atomic-sas.xvg
-rw-rw-r-- 1 Mass Mass 39542 Sep
1 21:56 #bLac_orig_md4-5_atomic-sas.xvg.1#
-rw-rw-r-- 1 Mass Mass 2360604 Sep
9 20:11 bLac_orig_md4-5_radius-of-gyration.xvg
-rw-rw-r-- 1 Mass Mass 2360602 Sep
1 21:02 #bLac_orig_md4-5_radius-of-gyration.xvg.1#
-rw-rw-r-- 1 Mass Mass 6135 Sep
9 20:54 bLac_orig_md4-5_residue-sas.xvg
-rw-rw-r-- 1 Mass Mass 6158 Sep
1 21:56 #bLac_orig_md4-5_residue-sas.xvg.1#
-rw-rw-r-- 1 Mass Mass 1098421 Sep
9 19:50 bLac_orig_md4-5_rmsd-Calpha-vs-start.xvg
-rw-rw-r-- 1 Mass Mass 1098406 Sep
1 19:37 #bLac_orig_md4-5_rmsd-Calpha-vs-start.xvg.1#
-rw-rw-r-- 1 Mass Mass 2815 Sep
9 20:00 bLac_orig_md4-5_rmsf-per-residue.xvg
-rw-rw-r-- 1 Mass Mass 2799 Sep
1 20:18 #bLac_orig_md4-5_rmsf-per-residue.xvg.1#
-rw-rw-r-- 1 Mass Mass 6739262 Sep
8 19:45 bLac_orig_md4-5_SecStruct.dat
-rw-rw-r-- 1 Mass Mass 2360697 Sep
9 20:54 bLac_orig_md4-5_solvent-accessible-surface.xvg
-rw-rw-r-- 1 Mass Mass 2360696 Sep
1 21:56 #bLac_orig_md4-5_solvent-accessible-surface.xvg.1#
-rw-rw-r-- 1 Mass Mass 9393557496 Sep
1 18:53 bLac_orig_md4-5.xtc
-rw------- 1 Mass Mass 1539720 Aug
21 06:19 bLac_orig_md4.cpt
-rw------- 1 Mass Mass 7561608 Aug
21 06:08 bLac_orig_md4.edr
-rw------- 1 Mass Mass 4412810 Aug
21 06:08 bLac_orig_md4.gro
-rw------- 1 Mass Mass 7212890 Aug
21 06:08 bLac_orig_md4.log
-rw------- 1 Mass Mass 1539720 Aug
21 04:58 bLac_orig_md4_prev.cpt
-rw------- 1 Mass Mass 2075808 Aug
21 06:08 bLac_orig_md4.tpr
-rw------- 1 Mass Mass 15351454992 Aug
21 06:19 bLac_orig_md4.trr
-rw------- 1 Mass Mass 2348637800 Aug
21 05:08 bLac_orig_md4.xtc
-rw------- 1 Mass Mass 1539720 Aug
21 04:58 bLac_orig_md5.cpt
-rw------- 1 Mass Mass 7561608 Aug
21 04:58 bLac_orig_md5.edr
-rw------- 1 Mass Mass 4412810 Aug
21 04:58 bLac_orig_md5.gro
-rw------- 1 Mass Mass 7212675 Aug
21 04:58 bLac_orig_md5.log
-rw------- 1 Mass Mass 1539720 Aug
21 06:08 bLac_orig_md5_prev.cpt
-rw------- 1 Mass Mass 2075808 Aug
21 04:58 bLac_orig_md5.tpr
-rw------- 1 Mass Mass 15351454992 Aug
21 06:08 bLac_orig_md5.trr
-rw------- 1 Mass Mass 2348549636 Aug
21 06:19 bLac_orig_md5.xtc
-rw------- 1 Mass Mass 10315 Aug
21 07:39 bLac_orig.p1n14-c.69215.err
-rw------- 1 Mass Mass 0 Aug
21 07:39 bLac_orig.p1n14-c.69215.out
-rw------- 1 Mass Mass 10312 Aug
21 06:31 bLac_orig.p1n14-c.69321.err
-rw------- 1 Mass Mass 0 Aug
21 06:31 bLac_orig.p1n14-c.69321.out
-rw------- 1 Mass Mass 10311 Aug
21 06:19 bLac_orig.p1n14-c.69391.err
-rw------- 1 Mass Mass 0 Aug
21 06:19 bLac_orig.p1n14-c.69391.out
-rw------- 1 Mass Mass 10323 Aug
21 06:08 bLac_orig.p1n14-c.69459.err
-rw------- 1 Mass Mass 0 Aug
21 06:08 bLac_orig.p1n14-c.69459.out
-rw-rw-r-- 1 Mass Mass 23567 Sep
8 19:46 bSheet.dat
-rw-rw-r-- 1 Mass Mass 492491 Sep
8 19:46 Coil.dat
-rw-rw-r-- 1 Mass Mass 1724 Sep
1 22:38 convertSecStruct.py
-rw-rw-r-- 1 Mass Mass 1726 Aug
23 19:16 convertSecStruct.py~
-rw------- 1 Mass Mass 0 Oct
11 11:48 dd12OZpQ
-rw------- 1 Mass Mass 0 Oct
8 22:31 dd1bJ83q
-rw------- 1 Mass Mass 0 Oct
9 18:15 dd2GqPRo
-rw------- 1 Mass Mass 0 Oct
9 11:43 dd3AQTim
-rw------- 1 Mass Mass 0 Oct
9 13:55 dd5izSa1
-rw-rw-r-- 1 Mass Mass 126585 Oct
9 22:18 dd5k95ba
-rw------- 1 Mass Mass 0 Oct
9 22:18 #dd5k95ba.1#
-rw-rw-r-- 1 Mass Mass 126571 Oct
10 00:05 dd5VY5Ob
-rw------- 1 Mass Mass 0 Oct
10 00:05 #dd5VY5Ob.1#
-rw-rw-r-- 1 Mass Mass 126580 Oct
11 00:06 dd63Ggfl
-rw------- 1 Mass Mass 0 Oct
11 00:06 #dd63Ggfl.1#
-rw------- 1 Mass Mass 0 Oct
9 12:40 dd6bmSfW
-rw-rw-r-- 1 Mass Mass 126580 Oct
9 12:40 dd6ciMJR
-rw------- 1 Mass Mass 0 Oct
9 12:40 #dd6ciMJR.1#
-rw------- 1 Mass Mass 0 Oct
9 11:52 dd7pgAvg
-rw------- 1 Mass Mass 0 Oct
11 12:11 dd81JqKw
-rw------- 1 Mass Mass 0 Oct
8 23:30 dd8P70pO
-rw------- 1 Mass Mass 0 Oct
9 16:13 dd9CPCaE
-rw------- 1 Mass Mass 0 Oct
12 10:21 dd9T7qxp
-rw-rw-r-- 1 Mass Mass 126601 Oct
10 18:13 ddAIUVdB
-rw------- 1 Mass Mass 0 Oct
10 18:13 #ddAIUVdB.1#
-rw------- 1 Mass Mass 0 Oct
9 17:39 ddbhwZ9W
-rw------- 1 Mass Mass 0 Oct
12 10:21 ddBJzg7d
-rw------- 1 Mass Mass 0 Oct
8 23:09 ddBKCOlE
-rw------- 1 Mass Mass 0 Oct
9 13:38 ddDeBqfS
-rw------- 1 Mass Mass 0 Oct
9 00:03 ddDw3nV1
-rw------- 1 Mass Mass 0 Oct
9 11:31 ddePESvy
-rw------- 1 Mass Mass 0 Oct
8 23:48 ddEpULbz
-rw------- 1 Mass Mass 0 Oct
11 11:48 ddf9JMgp
-rw------- 1 Mass Mass 0 Oct
9 16:57 ddFK42q2
-rw-rw-r-- 1 Mass Mass 126585 Oct
9 17:39 ddFk5bRK
-rw------- 1 Mass Mass 0 Oct
9 17:39 #ddFk5bRK.1#
-rw------- 1 Mass Mass 0 Oct
8 23:53 ddfnmwxE
-rw------- 1 Mass Mass 0 Oct
9 22:18 ddgbNwit
-rw------- 1 Mass Mass 0 Oct
11 00:06 ddgEtohC
-rw------- 1 Mass Mass 0 Oct
11 11:29 ddgqi2kq
-rw------- 1 Mass Mass 0 Oct
9 11:11 ddGZCbrR
-rw-rw-r-- 1 Mass Mass 126592 Oct
9 18:15 ddHfjrXf
-rw------- 1 Mass Mass 0 Oct
9 18:15 #ddHfjrXf.1#
-rw-rw-r-- 1 Mass Mass 126580 Oct
9 12:59 ddHukqLY
-rw------- 1 Mass Mass 0 Oct
9 12:59 #ddHukqLY.1#
-rw------- 1 Mass Mass 0 Oct
8 22:31 ddHYqKvW
-rw-rw-r-- 1 Mass Mass 126586 Oct
9 16:57 ddI56gOp
-rw------- 1 Mass Mass 0 Oct
9 16:57 #ddI56gOp.1#
-rw-rw-r-- 1 Mass Mass 126589 Oct
9 16:19 ddI87Z5K
-rw------- 1 Mass Mass 0 Oct
9 16:19 #ddI87Z5K.1#
-rw------- 1 Mass Mass 0 Oct
9 13:38 ddiNMqW4
-rw------- 1 Mass Mass 0 Oct
9 16:13 ddiPEmAw
-rw------- 1 Mass Mass 0 Oct
8 23:59 ddITfDpx
-rw------- 1 Mass Mass 0 Oct
8 23:53 ddIX0QPg
-rw------- 1 Mass Mass 0 Oct
8 23:15 ddjex0J9
-rw-rw-r-- 1 Mass Mass 126580 Oct
9 13:55 ddjjHt6D
-rw------- 1 Mass Mass 0 Oct
9 13:55 #ddjjHt6D.1#
-rw------- 1 Mass Mass 0 Oct
9 12:59 ddjJuFHJ
-rw-rw-r-- 1 Mass Mass 126589 Oct
9 15:11 ddKHcEaq
-rw------- 1 Mass Mass 0 Oct
9 15:11 #ddKHcEaq.1#
-rw------- 1 Mass Mass 0 Oct
11 12:11 ddlna4cU
-rw------- 1 Mass Mass 0 Oct
9 13:37 ddmGeKiP
-rw------- 1 Mass Mass 0 Oct
10 00:05 ddn0nbbw
-rw------- 1 Mass Mass 0 Oct
12 01:07 ddnGnkgn
-rw------- 1 Mass Mass 0 Oct
8 23:48 ddOs3USU
-rw-rw-r-- 1 Mass Mass 126601 Oct
9 11:48 ddP3yZzs
-rw------- 1 Mass Mass 0 Oct
9 11:48 #ddP3yZzs.1#
-rw------- 1 Mass Mass 0 Oct
8 22:39 ddpVeYNy
-rw-rw-r-- 1 Mass Mass 126601 Oct
9 11:11 ddPywpnQ
-rw------- 1 Mass Mass 0 Oct
9 11:11 #ddPywpnQ.1#
-rw-rw-r-- 1 Mass Mass 126584 Oct
11 00:32 ddQ0FCUF
-rw------- 1 Mass Mass 0 Oct
11 00:32 #ddQ0FCUF.1#
-rw------- 1 Mass Mass 0 Oct
8 23:59 ddQf5OpS
-rw------- 1 Mass Mass 0 Oct
9 15:11 ddrbJTXC
-rw------- 1 Mass Mass 0 Oct
9 00:01 ddsVTsbQ
-rw------- 1 Mass Mass 0 Oct
12 01:07 ddt9BOGS
-rw------- 1 Mass Mass 0 Oct
9 13:38 ddtm5ddy
-rw-rw-r-- 1 Mass Mass 126562 Oct
8 23:30 ddToe9c5
-rw------- 1 Mass Mass 0 Oct
8 23:30 #ddToe9c5.1#
-rw------- 1 Mass Mass 0 Oct
9 16:19 ddtOS4T8
-rw------- 1 Mass Mass 0 Oct
8 23:09 ddTqDyMy
-rw------- 1 Mass Mass 0 Oct
11 11:54 ddU3FPrI
-rw------- 1 Mass Mass 0 Oct
9 13:37 dduAteao
-rw-rw-r-- 1 Mass Mass 126590 Oct
8 23:33 ddUVYvY6
-rw------- 1 Mass Mass 0 Oct
8 23:33 #ddUVYvY6.1#
-rw-rw-r-- 1 Mass Mass 126571 Oct
9 11:31 ddVELpdp
-rw------- 1 Mass Mass 0 Oct
9 11:31 #ddVELpdp.1#
-rw------- 1 Mass Mass 0 Oct
8 23:33 ddVs5Ir3
-rw------- 1 Mass Mass 0 Oct
11 11:54 ddvtG57T
-rw-rw-r-- 1 Mass Mass 126577 Oct
9 11:52 ddvXXILu
-rw------- 1 Mass Mass 0 Oct
9 11:52 #ddvXXILu.1#
-rw-rw-r-- 1 Mass Mass 126562 Oct
8 23:29 ddWCQIOU
-rw------- 1 Mass Mass 0 Oct
8 23:29 #ddWCQIOU.1#
-rw------- 1 Mass Mass 0 Oct
8 23:29 ddwNnmjX
-rw------- 1 Mass Mass 0 Oct
8 22:39 ddxgc6ku
-rw------- 1 Mass Mass 0 Oct
9 11:48 ddXvoe3O
-rw------- 1 Mass Mass 0 Oct
9 11:43 ddY88BZ1
-rw------- 1 Mass Mass 0 Oct
11 11:29 ddYDrUtV
-rw-rw-r-- 1 Mass Mass 126571 Oct
9 13:38 ddyV47ss
-rw------- 1 Mass Mass 0 Oct
9 13:38 #ddyV47ss.1#
-rw------- 1 Mass Mass 0 Oct
9 00:03 ddYZwGgr
-rw------- 1 Mass Mass 0 Oct
9 00:01 ddZ3W86W
-rw------- 1 Mass Mass 0 Oct
10 18:13 ddzCJGlM
-rw-rw-r-- 1 Mass Mass 126576 Oct
8 23:15 ddZGP3ET
-rw------- 1 Mass Mass 0 Oct
8 23:15 #ddZGP3ET.1#
-rw------- 1 Mass Mass 0 Oct
11 00:32 ddzUlAvc
-rw------- 1 Mass Mass 3608 Aug
21 07:39 decane_817.top
-rw-rw-r-- 1 Mass Mass 934806 Sep
8 19:46 Extended.dat
-rw------- 1 Mass Mass 2348579612 Aug
21 06:30 md2-3.xtc
-rw------- 1 Mass Mass 1955 Aug
21 07:39 md2.mdp
-rw------- 1 Mass Mass 1955 Aug
21 06:31 md3.mdp
-rw------- 1 Mass Mass 1955 Aug
21 06:08 md4.mdp
-rw------- 1 Mass Mass 1955 Aug
21 06:08 md5.mdp
-rw------- 1 Mass Mass 10416 Aug
21 06:31 mdout.mdp
-rw------- 1 Mass Mass 10416 Aug
21 06:31 #mdout.mdp.1#
-rw------- 1 Mass Mass 10416 Aug
21 06:19 #mdout.mdp.2#
-rw------- 1 Mass Mass 10416 Aug
21 06:19 #mdout.mdp.3#
-rw------- 1 Mass Mass 10416 Aug
21 06:19 #mdout.mdp.4#
-rw-rw-r-- 1 Mass Mass 0 Sep
8 19:46 piHelix.dat
-rw------- 1 Mass Mass 29 Aug
21 06:19 proc_vs_time
-rw-rw-r-- 1 Mass Mass 583444 Sep
9 20:13 Radius of gyration 200ns
-rw------- 1 Mass Mass 3074724 Aug
21 07:39 result_md1.cpt
-rw------- 1 Mass Mass 723840 Aug
21 07:39 result_md1.edr
-rw------- 1 Mass Mass 4412810 Aug
21 07:39 result_md1.gro
-rw------- 1 Mass Mass 117657676 Aug
21 07:39 result_md1.xtc
-rw-rw-r-- 1 Mass Mass 663500 Sep
9 19:52 RMSD original
-rw-rw-r-- 1 Mass Mass 11761 Sep
9 20:01 RMSF original
-rw------- 1 Mass Mass 783 Aug
21 07:39 run_gromacs.ll
-rw-rw-r-- 1 Mass Mass 2307423 Sep
9 21:00 SASA 200ns
-rw-rw-r-- 1 Mass Mass 2502373 Sep
9 00:05 Secondary Structure analysis original
-rw-rw-r-- 1 Mass Mass 753766 Sep
8 19:46 Turn.dat
On Sunday, October 13, 2013 11:13 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
On 10/12/13 6:08 PM, Mass wrote:
> Dear users;
> I am trying to run DSSP and have problem, I typed in terminal
> do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump
>
>
> and got the following error,
>
> Program do_dssp, VERSION 4.6.3
> Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524
>
> Can not open file:
> bLac_orig_md2.trr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I can see the file bLac_orig_md2.trr in the directory
>
> any comments?
>
Please provide the copied and pasted output of ls -l in that directory.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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