[gmx-users] do_dssp file format
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Mon Jan 14 12:06:18 CET 2008
Hi Gromacs users
After many try this weekend with my problem with do_dssp I come back to the mailing list
First, as David said me last friday in a previous message I have test my dssp program with example of pdb file from the Protein Data Bank (1HRC) (with one protein configuration in it)
It works ! the calculation of the secondary structure is made and i obtain an output.
When i use this pdb with do_dssp with the following command
/applications/gromacs-3.3.2-fftw/bin/do_dssp -s test_template.pdb -f test_template.pdb -o ss.xpm
I obtain the menu and I choose 5 (MainChain)
I obtained the follwing message:
There are 103 residues in your selected group
Opening library file /applications/gromacs-3.3.2-fftw/share/gromacs/top/ss.map
Reading frame 0 time -1.000
Back Off! I just backed up ddEG4D6s to ./#ddEG4D6s.1#
And the calculation is not made (I wait more than ten minutes) and i obtain no ss.xpm
I dont understand what is the problem
Thank you again for your help
Stefane
> 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>
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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.
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>
>
>
>
> ------------------------------
>
> 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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>
========================================
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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