[gmx-users] [Fwd: How simulate two peptides in a box?]

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 2 05:55:56 CEST 2007

Hi Fufeng Liu,

I guess you ran pdb2gmx on the two peptides, where both peptides had
the same chain identifiers. In that case, pdb2gmx will assume that
it's one molecule and connect them. Use chain identifiers to indicate
the different peptides, or build topologies first on separate files
and combine the peptides later.



On 7/1/07, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> Please keep requests for help on the list. That way they're archived for
> others to use, and other people can raise points of interest.
> The last sentence here
> http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off
> is my suggestion for you :-) Probably, you have only one [molecule]
> statement for your two molecules, and by chance you included it first so
> that there was no error message from grompp. If you don't understand why
> this is a problem, find the relevant section of Chapter 5 of the manual -
> or read the whole lot of that chapter! :-)
> Mark
> ---------------------------- Original Message ----------------------------
> Subject: How simulate two peptides in a box?
> From:    fufengliu at tju.edu.cn
> Date:    Sun, July 1, 2007 11:09 pm
> To:      mark.abraham at anu.edu.au
> --------------------------------------------------------------------------
> Dear Mark:
>      I'm a graduate student at Tianjin University. I want to simulate two
> peptides
> in a box using GROMACS software? I followed your suggestion
> {set up your topologies (suggest one molecule in each of two .itp files)
> #include them in the .top file, pick a starting configuration for both of
> them in the same structure file, solvate, minimize.}
> But when I minimized the system, I got the information ¡±1-4 interaction
> between 83 and 85 at distance 1.862 which is larger than the 1-4 table
> size 1.000 nm¡±. I checked the topology and found that atom 83 belong to
> one peptide and the atom 85 the other peptide. That¡¯s to say the two
> peptides were considered as a peptide. Can you tell me how to do?  I'd be
> very happy and grateful if you could tell me how to do it.
> Looking forward to your reply.
>      Best regards.
>              Fufeng Liu
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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