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

Mark Abraham mark.abraham at anu.edu.au
Sun Jul 1 16:11:35 CEST 2007

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
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! :-)


---------------------------- 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
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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