[gmx-users] do_dssp file format
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Fri Jan 11 18:54:45 CET 2008
I am back :(
The procedure i did
1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm
The menu appears I choose 5 (Main Chain) and I obtained the following message
--------
GROningen MAchine for Chemical Simulation
:-) VERSION 3.3.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) /applications/gromacs-3.3.1-fftw/bin/do_dssp (-:
Option Filename Type Description
------------------------------------------------------------
-f test-Struc.pdb Input Generic trajectory: xtc trr trj gro g96 pdb
-s test-Struc.pdb Input Structure+mass(db): tpr tpb tpa gro g96 pdb
xml
-n index.ndx Input, Opt. Index file
-ssdump ssdump.dat Output, Opt. Generic data file
-map ss.map Input, Lib. File that maps matrix data to colors
-o ss.xpm Output X PixMap compatible matrix file
-sc scount.xvg Output xvgr/xmgr file
-a area.xpm Output, Opt. X PixMap compatible matrix file
-ta totarea.xvg Output, Opt. xvgr/xmgr file
-aa averarea.xvg Output, Opt. xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 1 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: ps, fs, ns, us, ms or s
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-sss string HEBT Secondary structures for structure count
Opening library file /applications/gromacs-3.3.1-fftw/share/gromacs/top/phbres.dat
Opening library file /applications/gromacs-3.3.1-fftw/share/gromacs/top/aminoacids.dat
Group 0 ( System) has 1674 elements
Group 1 ( Protein) has 1623 elements
Group 2 ( Protein-H) has 796 elements
Group 3 ( C-alpha) has 101 elements
Group 4 ( Backbone) has 304 elements
Group 5 ( MainChain) has 405 elements
Group 6 (MainChain+Cb) has 494 elements
Group 7 ( MainChain+H) has 405 elements
Group 8 ( SideChain) has 1218 elements
Group 9 ( SideChain-H) has 391 elements
Group 10 ( Prot-Masses) has 1623 elements
Group 11 ( Non-Protein) has 51 elements
Group 12 ( HSD) has 51 elements
Group 13 ( Other) has 51 elements
I select a group: 5
Selected 5: 'MainChain'
There are 102 residues in your selected group <--- OK for me
Opening library file /applications/gromacs-3.3.1-fftw/share/gromacs/top/ss.map
Reading frame 0 time -1.000
Back Off! I just backed up ddsGGvys to ./#ddsGGvys.1#
The ddsGGvys is indeed a pdb file with the protein atoms (main chain). But the program seems to run because the prompt did not appear but the ouput ss.xpm is never present.
What is the problem ?
Thank you
> Thanks Justin for your reply
>
> So I used the choice 5(MainChain), 6(MainChain+Cb) and 7(MainChain+H)to test.
> I obtained always the same error.
>
> Opening library file /applications/gromacs-3.2.1/share/top/ss.map
> Reading frame 0 time -1.000
> Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#
What error? It appears that do_dssp is backing up an old intermediate file that
gets generated as part of the calculation.
-Justin
>
> Note that the pdb seems correct because the secondary structure can be
> obtained with Stride available in VMD. And my trajectory was made CHARMM
> ffield. is this a problem in this case
>
> Thank a lot
>
> My story with do_dssp
>
> As suggested David and others i rename my pdb file with the extension .pdb
>
> i used the following command
>
> ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb
>
> A menu appears, I choose the group 1 (protein) and i obtained the error
> message
>
> Opening library file /applications/gromacs-3.2.1/share/top/ss.map
> Reading frame 0 time -1.000
> Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1#
>
> What iis the problem. I give below a part of my pdb file
>
> ATOM 1 CAY ACE 1 6.421 -7.877 -11.574 -0.27 0.00
> ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00
> ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00
> ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00
> ATOM 5 C ACE 1 7.470 -8.140 -10.510 0.51 0.00
> ATOM 6 O ACE 1 7.594 -9.280 -10.074 -0.51 0.00
> ATOM 7 N GLY 2 8.125 -7.096 -10.030 -0.47 0.00
> ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00
> ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00
> ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00
> ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00
> ATOM 12 C GLY 2 10.408 -6.734 -9.033 0.51 0.00
> ATOM 13 O GLY 2 11.313 -7.365 -8.492 -0.51 0.00
> ATOM 14 N ASP 3 10.647 -5.532 -9.599 -0.47 0.00
> ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00
> ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00
> ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00
> ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00
> ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00
> ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00
> ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00
> ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00
> ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00
>
> Thank you again for your kindly help
>
> Stefane
>
> ABEL Stephane 175950 wrote:
> > I used the following command
> >
> > ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a
> part is show below. I obtained a segmentation fault.
> >
> > Maybe it is not a the good command. Remember that my trajectories are not
> made/compatible with GROMACS and i have only a pdb coordinates of my MD.
> >
> don't rename the .pdb file to .tpr. Just use .pdb
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 11 Jan 2008 09:30:47 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: Targeted MD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47869C97.8020903 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Steven Kirk wrote:
> > Mark Abraham <Mark.Abraham at anu.edu.au> wrote
>
> >> "Non-Protein" serves well here. So a usual tc-grps line has "Protein
> >> Non-Protein" for a protein simulation.
> >>
> >> Mark
> >
> > A supplementary question.
> >
> > The tc-grps line can take predefined standard group names such as
> > 'System', 'Protein' and 'Non-Protein'.
> >
> > Does the 'Protein' group need to actually BE a protein, or are 'Protein'
> > and 'Non-Protein' really synonyms for
> > 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ?
>
> I haven't read the code or found any mention in the manual, but I expect
> that src/share/top/aminoacids.dat contains the names of any amino acids,
> and thus implicitly defines these groups.
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 11 Jan 2008 09:24:40 +0800
> From: "xuji"<xuji at home.ipe.ac.cn>
> Subject: [gmx-users] Asking help about PME
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID: <20080111011325.39420249A7A at home.ipe.ac.cn>
> Content-Type: text/plain; charset="gb2312"
>
> Hi all gromacs users:
>
> I am digging into the PME method in gromacs. Can someone tell
> me what files have something to do with PME and the corresponding
> method FFT?
>
> Thanks!
> ¡¡¡¡
>
>
> Best wishes!
>
> Ji Xu
> Institute of Process Engineering
> Chinese Academy of Sciences
> P.O.Box 353, Beijing, 100080, China
> Tel: +86-10-82627076
> Fax:+86-10-62558065
> xuji at home.ipe.ac.cn
>
> 2008-01-11
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
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>
> Message: 4
> Date: Fri, 11 Jan 2008 13:10:11 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Asking help about PME
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4786D003.5020206 at anu.edu.au>
> Content-Type: text/plain; charset=GB2312
>
> xuji wrote:
> >
> > Hi all gromacs users:
> >
> > I am digging into the PME method in gromacs. Can someone tell
> > me what files have something to do with PME and the corresponding
> > method FFT?
>
> >From the gromacs source directory, try
>
> find * -name "*pme*"
>
> and
>
> grep -i pme src/*/*.c include/*.h include/*/*.h | grep -v -i development
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 11 Jan 2008 10:44:05 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: [gmx-users] Asking help about PME
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4786D7F5.6030908 at yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
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> ------------------------------
>
> Message: 6
> Date: Fri, 11 Jan 2008 09:55:19 +0530 (IST)
> From: kinshuk at chem.iitb.ac.in
> Subject: [gmx-users] (no subject)
> To: gmx-users at gromacs.org
> Message-ID:
> <1073.10.103.134.66.1200025519.squirrel at www.chem.iitb.ac.in>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi all,
> I have been trying to generate .rtp, .top files from having input of .gro
> file for particular molecule in gromacs. I tried this with (x2top) command
> implemented in gromacs but i have encountered a problem while executing
> this command , that i am mentioning below.
>
> Fatal error: Library file ffG43a1.n2t not found in current dir nor in
> default directories.
> (You can set the directories to search with the GMXLIB path variable.)
>
> So how do i will be able to resolve this problem.
> If i will be getting any help i will be very thankful for you.
>
> Kinshuk Raj Srivastava
> IIT-Bombay
> India
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 11 Jan 2008 10:02:06 +0530 (IST)
> From: kinshuk at chem.iitb.ac.in
> Subject: [gmx-users] x2top & Library file ffG43a1.n2t
> To: gmx-users at gromacs.org
> Message-ID:
> <1090.10.103.134.66.1200025926.squirrel at www.chem.iitb.ac.in>
> Content-Type: text/plain;charset=iso-8859-1
>
>
> Hi all,
> I have been trying to generate .rtp, .top files from having input of .gro
> file for particular molecule in gromacs. I tried this with (x2top) command
> implemented in gromacs but i have encountered a problem while executing
> this command , that i am mentioning below.
>
> Fatal error: Library file ffG43a1.n2t not found in current dir nor in
> default directories.
> (You can set the directories to search with the GMXLIB path variable.)
>
> So how do i will be able to resolve this problem.
> If i will be getting any help i will be very thankful for you.
>
> Kinshuk Raj Srivastava
> IIT-Bombay
> India
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Fri, 11 Jan 2008 16:23:52 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] (no subject)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4786FD68.5010909 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> kinshuk at chem.iitb.ac.in wrote:
> > Hi all,
> > I have been trying to generate .rtp, .top files from having input of .gro
> > file for particular molecule in gromacs. I tried this with (x2top) command
> > implemented in gromacs but i have encountered a problem while executing
> > this command , that i am mentioning below.
> >
> > Fatal error: Library file ffG43a1.n2t not found in current dir nor in
> > default directories.
> > (You can set the directories to search with the GMXLIB path variable.)
> >
> > So how do i will be able to resolve this problem.
> > If i will be getting any help i will be very thankful for you.
>
> So what value does GMXLIB have? What value should it have? Where did you
> install GROMACS? Can you find this file anywhere? Have you read the
> x2top documentation?
>
> Mark
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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>
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> *****************************************
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>
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
------------------------------
Message: 2
Date: Fri, 11 Jan 2008 11:01:58 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] chromophore parameters for Molecular
Dynamics
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <1200067318.478792f6cc45f at webmail.vt.edu>
Content-Type: text/plain; charset=ISO-8859-1
Quoting Anthony Cruz <acb15885 at uprm.edu>:
> Hi users:
> I am working in a new projec and we plan to do some molecular dynamic
> experiment to an engineered GFP molecule. I have been searching for the
> parameters for the GFP chromophore without success. Can some one help me? Any
> reference or parameters??
Unless someone has already developed them, you'll have to do it yourself (not an
easy task). See here:
http://wiki.gromacs.org/index.php/Exotic_Species
and
http://wiki.gromacs.org/index.php/Parameterization
-Justin
>
> Best Regards,
> Anthony
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
------------------------------
Message: 3
Date: Fri, 11 Jan 2008 12:34:51 -0500
From: "Myunggi Yi" <myunggi at gmail.com>
Subject: [gmx-users] Re: Invalid order for directive defaults
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<ef0ebd150801110934w551da25cjd474c861d887a1c9 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
I solved the problem.
I found one more "ffgmx.itp" in my pro.itp.
On Jan 11, 2008 12:29 PM, Myunggi Yi <myunggi at gmail.com> wrote:
> Dear gromca users,
>
> I'm a new user of gromacs.
> I'm trying to run energy minimization on the system of a short peptide and
> a lipid bilayer.
> The following is my top file.
>
> ++++++++++++++++++++
> ;
> #include "ffgmx.itp"
> #include "../lipid.popc.itp"
> #include "popc.itp"
> #include "pro.itp"
> #include "ions.itp"
> #include "spc.itp"
>
>
> [ system ]
> ; name
> Fusion peptide on POPC
>
> [ molecules ]
> ; name number
> Protein 1
> POPC 128
> Na 2
> SOL 3655
> +++++++++++++++++++
>
>
>
> And I copied em.mdp with a little modification from the tutorial.
>
>
>
> +++++++++++++++++++
> ; User spoel (236)
> ; Wed Nov 3 17:12:44 1993
> ; Input file
> ;
> cpp = cpp
> define = -DPOSRES
> constraints = none
> integrator = steep
> nsteps = 100
> ;
> ; Energy minimizing stuff
> ;
> emtol = 2000
> emstep = 0.01
>
> nstcomm = 1
> ns_type = grid
> rlist = 1
> rcoulomb = 1.0
> rvdw = 1.0
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> ++++++++++++++++++
>
>
> After runing grompp I've got the following error message.
>
>
> ++++++++++++++++++++++
> Program grompp, VERSION 3.3.1
> Source code file: topio.c, line: 388
>
> Fatal error:
> Invalid order for directive defaults, file
> ""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"",
> line 4
> ++++++++++++++++++++
>
> I think I have only one [ defaults ] section.
> Does Anybody have an idea? What is wrong?
>
> Have a great day.
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi>
--
Best wishes,
MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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Message: 4
Date: Fri, 11 Jan 2008 12:29:59 -0500
From: "Myunggi Yi" <myunggi at gmail.com>
Subject: [gmx-users] Invalid order for directive defaults
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
<ef0ebd150801110929w251a2604qf5f12fbad3ed7d31 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear gromca users,
I'm a new user of gromacs.
I'm trying to run energy minimization on the system of a short peptide and a
lipid bilayer.
The following is my top file.
++++++++++++++++++++
;
#include "ffgmx.itp"
#include "../lipid.popc.itp"
#include "popc.itp"
#include "pro.itp"
#include "ions.itp"
#include "spc.itp"
[ system ]
; name
Fusion peptide on POPC
[ molecules ]
; name number
Protein 1
POPC 128
Na 2
SOL 3655
+++++++++++++++++++
And I copied em.mdp with a little modification from the tutorial.
+++++++++++++++++++
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
cpp = cpp
define = -DPOSRES
constraints = none
integrator = steep
nsteps = 100
;
; Energy minimizing stuff
;
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
++++++++++++++++++
After runing grompp I've got the following error message.
++++++++++++++++++++++
Program grompp, VERSION 3.3.1
Source code file: topio.c, line: 388
Fatal error:
Invalid order for directive defaults, file
""/panfs/storage.local/scs/home/myunggi/gromacs-openmpi/share/gromacs/top/ffgmx.itp"",
line 4
++++++++++++++++++++
I think I have only one [ defaults ] section.
Does Anybody have an idea? What is wrong?
Have a great day.
--
Best wishes,
MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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