[gmx-users] RE : gmx-users Digest, Vol 45, Issue 36

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 11 16:58:23 CET 2008 

Quoting ABEL Stephane 175950 <Stephane.ABEL at cea.fr>:

> 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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>
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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
>
>
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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
>
>
> ------------------------------
>
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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/

========================================

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