[gmx-users] a question about pepetide chains interaction

Wang Zhun wangzhun at pumc.edu.cn
Sat Dec 17 17:02:42 CET 2005


Yes. I generated a pdb file containing the two peptides and named them with different identifier by DeepView.Then I generated the gro and top file from the pdb structure. And I made the index file by make_ndx to specify the two peptides before MD simulation.
Sound reasonable? I don't know how to combine and edit the two separate top files as previous stated in the maillist, so I turn to this "alternative", hoping this will work. 


In your mail:
>From: <leafyoung81-group at yahoo.com>
>Reply-To: leafyoung81-group at yahoo.com,
Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] a question about pepetide chains interaction
>Date:Sat, 17 Dec 2005 07:13:31 -0800 (PST)
>
>"generate the structure with two pepetides in one file and name each with different identifier"
>
>I am not clear about this. Generate one topologies or one .gro file?
>
>As long as, in [ molecules ] sections, there are separated entry to each chain, it is fine.
>
>Yang Ye
>
>Wang Zhun <wangzhun at pumc.edu.cn> wrote: Hi, all,
>
>If I want to simulate the interaction between two peptides, based on previous mailling posts, I should generate two separate .gro structures and .top topologies for each pepetide and combine them for further MD simulation.
>Now I wonder if I generate the structure with two pepetides in one file and name each with different identifier, can I carry MD simulation in a way of simulation of protein with multiple subunits in the FAQ?
>
>Thanks!
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