[gmx-users] a question about pepetide chains interaction

[David van der Spoel]

Wang Zhun wrote:
> 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 ed
with a text editor.


it 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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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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