[gmx-users] How to include FE2+ in ions.itp ?

Tanos Franca tanos at ime.eb.br
Wed Jan 5 14:26:45 CET 2011

     Dear GROMACS users,
     We're trying to perform a MD simulation of a system with a hematin 
group but realized that GROMACS does not have parameters for the ion 
FE2+. We tried to include the parametrs in the file ions.itp but did not 
suceed yet. Does anybody knows the right procedure to introduce this 
ions into the file ions.itp ? Do we have to change anything more in 
order to GROMACS recognize the new ion ?
     With my best regards,
     Tanos C. C. Franca.
     Coordinator of the Graduate Program in Chemistry
     Military Institute of Engineering.
     Rio de Janeiro/RJ

Em 05/01/2011 10:47, gmx-users-request at gromacs.org escreveu:
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>     1. Re: Library file in.m2p not found (Justin A. Lemkul)
>     2. Warning about (short) potential interruption - moving	DNS
>        servers for gromacs.org (Erik Lindahl)
>     3. Re: Library file in.m2p not found (ahmet y?ld?r?m)
>     4. HFIP solvent box... (sharada)
>     5. Re: HFIP solvent box... (Justin A. Lemkul)
> ----------------------------------------------------------------------
> Message: 1
> Date: Wed, 05 Jan 2011 06:45:52 -0500
> From: "Justin A. Lemkul"<jalemkul at vt.edu>
> Subject: Re: [gmx-users] Library file in.m2p not found
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
> Message-ID:<4D2459F0.2020502 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-9; format=flowed
> ahmet yýldýrým wrote:
>> Dear Mark,
>> I am using the Gromacs on the Ubuntu for month but have not encountered
>> any problems.I did a search in the file system of Ubuntu. I do not have
>> a GMXLIB folder in a file system.
>> What should I do?
> If you're telling xpm2ps to use in.m2p, that file has to exist somewhere.  The
> error message is telling you that it does not exist in the working directory
> (i.e., the directory where you're issuing the command), or the standard Gromacs
> library directory
> (http://www.gromacs.org/Documentation/Terminology/Environment_Variables#GMXLIB).
> If you tell any Gromacs tool to use certain input, it has to exist; Gromacs
> isn't going to magically create all the proper files for you.
> -Justin
>> 05 Ocak 2011 10:42 tarihinde Mark Abraham<Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>>  yazdý:
>>      On 5/01/2011 7:37 PM, ahmet yýldýrým wrote:
>>          Dear users,
>>          I receive the following error when I entered the command "xpm2ps
>>          -f ss.xpm -o ss.eps -di in.m2p"
>>          Fatal error:
>>          Library file in.m2p not found in current dir nor in default
>>          directories.
>>          (You can set the directories to search with the GMXLIB path
>>          variable)
>>          I am using the Gromacs 4.05 on the Ubuntu 9.1 Operation System.
>>          I installed the Gromacs from Synaptic Package Manager.
>>          I used echo $GMXDATA but it did not show anything. The pdb2gmx,
>>          g_gyrate,...etc files are in the directory /usr/bin/.
>>          The GMXRC file is in the directory
>>          /usr/share/gromacs/shell-specific.
>>      Are you following these instructions?
>>      http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
>>      Mark
>>      --
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