[gmx-users] do_dssp file format

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Fri Jan 11 16:24:47 CET 2008


My story with do_dssp continues...https://webmail.cea.fr/Exchange/Stephane.ABEL/Bo%C3%AEte%20de%20r%C3%A9ception/?Cmd=contents&Page=1
 Boîte de réception 

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


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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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