[gmx-users] Ligand bond

[Andrea Carotti]

Dear Abel,
    If I'm not wrong, you must add the bond using a file called 
specbond.dat. By default, the file used is in the gromacs path, but you can 
modify it and make a copy in the directory when you're working on. You must 
specify the atom name, the interacting  residue and ligand names, and the 
distance between them. If everything goes fine, you will see during the 
preparation steps (perhaps grompp...i don't remember well) the link 
creation.
Hope this help
Andrea

----- Original Message ----- 
From: "abelius" <abelius at gmail.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, October 19, 2005 11:38 AM
Subject: Re: [gmx-users] Ligand bond


> It's a covalent bond. When I look at the .gro file before EM the bond is 
> there, after EM it no longer is ...
> Grompp Doesn't give any warnings.
>
>
> David Mobley wrote:
>
>> The "bond"? Is it covalently bound? If not, what do you mean? Do you get 
>> any warnings when you run grompp?
>>
>> On 10/18/05, *abelius* < abelius at gmail.com <mailto:abelius at gmail.com>> 
>> wrote:
>>
>>     Dear all,
>>
>>     I'm trying to run a simulation of a ligand bound to an enzyme. To
>>     produce the *.itp I used the PRODRG server.
>>     All goes well a first, but when I try to do an EM the bond between
>>     enzyme and protein breaks.
>>
>>     Does anyone knows how I can fix this ?
>>
>>     thx in advance,
>>
>>     Abel
>>
>>
>>     _______________________________________________
>>     gmx-users mailing list
>>     gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>>     http://www.gromacs.org/mailman/listinfo/gmx-users
>>     Please don't post (un)subscribe requests to the list. Use the
>>     www interface or send it to gmx-users-request at gromacs.org
>>     <mailto:gmx-users-request at gromacs.org>.
>>
>>
>>------------------------------------------------------------------------
>>
>>_______________________________________________
>>gmx-users mailing list
>>gmx-users at gromacs.org
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please don't post (un)subscribe requests to the list. Use the www 
>>interface or send it to gmx-users-request at gromacs.org.
>>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.