[gmx-users] RE: gmx-users Digest, Vol 88, Issue 46

[intra\sa175950]

Thank you Mark for the commands. It is indeed what I want. 

Stephane

On 9/08/2011 10:23 PM, intra\sa175950 wrote:
>
> Dear All,
>
> For verification purposes, I would like to obtain in a readable format 
> the list of the pairtypes values for a molecule generated by grompp 
> when the gen-pairs directive is set to "yes" in forcefield.itp file. 
>  It is possible ? If yes, how?
>

I'm not quite sure what you are seeking, but either grompp -pp or the 
interaction list in gmxdump of the resulting .tpr will have enough detail.

Note that atom numbering starts from zero in the latter, and it is not 
that easy to read. There will be a list of pair interactions that has 
numbers for each pair interaction that are indices into some other list 
of the types of such interactions. You may be best served by simplifying 
the system somehow.

Mark

> Thank you in advance for your response
>
> Stephane
>
>
>

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Message: 5
Date: Tue, 9 Aug 2011 11:03:26 -0300
From: C?sar ?vila <clavila at gmail.com>
Subject: [gmx-users] git release-4-5-patches behind proxy
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
	<CAKz=r7LQpktz5dx-6jMuYnwyxVWhcnp_tCzyAX_B0mCetra1vg at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

I want to calculate secondary structure propensities of residues.

Following Mark's message on thread
Re: [gmx-users] secondary structure propensities of residues


I would like to get the release-4.5-patches from git (in order to get
do_dssp.c). Nevertheless I found problems while trying to fetch it from git
repository due to the proxy. (I followed the advices on
http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Git_behind_a_proxy

$ git clone git://git.gromacs.org/gromacs.git
Initialized empty Git repository in ~/gromacs/.git/
2011/08/09 10:37:46 socat[17264] E CONNECT git.gromacs.org:9418: Forbidden
fatal: The remote end hung up unexpectedly

I tried the alternative suggested by Roland

git clone  http://repo.or.cz/r/gromacs.git
Initialized empty Git repository in ~/gromacs/.git/

The gromacs directory is created and populated. After this I ran

$git branch
* master

$git checkout --track -b release-4-5-patches origin/release-4-5-patches
fatal: git checkout: updating paths is incompatible with switching branches.
Did you intend to checkout 'origin/release-4-5-patches' which can not be
resolved as commit?

Is this a problem of the server I am using or is it just a misuse of git?

Thanks








2011/3/22 Roland Schulz <roland at utk.edu>

> you can clone from http://repo.or.cz/r/gromacs.git if you have problems
> with a proxy.
>
> On Mon, Mar 21, 2011 at 10:54 PM, Alif M Latif
<prism_dead at yahoo.com>wrote:
>
>>    Dear Gromacs Developers,
>>
>> Just dropping by to say THANK YOU for v4.5.4, surely is updated version
of
>> 4.5.3 with all the bugfixes yes?. I'm having problem getting past my
>> university's proxy server to use git. Now hopefully I can continue my
>> research and solve git problems later..Your hard work is greatly
>> appreciated!
>>
>> MUHAMMAD ALIF MOHAMMAD LATIF
>> Laboratory of Theoretical and Computational Chemistry
>> Department of Chemistry
>> Faculty of Science
>> Universiti Putra Malaysia
>> 43400 UPM Serdang, Selangor
>> MALAYSIA
>>
>>
>>
>> --
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>
>
>
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