again.
-Original Message-
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Mon, 31 Mar 2008 17:41:50 -0400
Subject: Re: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in
GROMACS
Quoting OZGE ENGIN <[EMAIL PROTECTED]
x27;ve
> built, something from the RCSB, etc?
>
> Have a look at your structure and the mdrun output (md.log, in particular) to
> see if you can determine where things are falling apart based on specific
> warnings (LINCS, etc.)
>
> -Justin
>
> >
> > -Origi
or GROMACS users
Date: Mon, 31 Mar 2008 15:25:11 -0400
Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN <[EMAIL PROTECTED]>:
> I already indicated the problem that I have. If I put an N prefix to the
> first residue, I get warning of
t based on specific
warnings (LINCS, etc.)
-Justin
>
> -Original Message-
> From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
> To: Discussion list for GROMACS users
> Date: Mon, 31 Mar 2008 14:42:55 -0400
> Subject: Re: [gmx-users] error with pdb2gmx wh
ce for the force on atoms.
-Original Message-
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Mon, 31 Mar 2008 14:42:55 -0400
Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS
Quoting OZGE ENGIN <[EMAIL PRO
Quoting OZGE ENGIN <[EMAIL PROTECTED]>:
> Hi all,
>
> I am trying to use AMBER ff in GROMACS. I have followed the steps that are
> given in the http://chemistry.csulb.edu/ffamber/ link.
>
> The first residue of the protein is GLN. I put an N prefix to this residue.
> The pdg2gmx works well excep
Hi all,
I am trying to use AMBER ff in GROMACS. I have followed the steps that are
given in the http://chemistry.csulb.edu/ffamber/ link.
The first residue of the protein is GLN. I put an N prefix to this residue. The
pdg2gmx works well except giving an warning of long bond between some ato
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