AMBER Archive (2008)

Subject: Re: AMBER: big molecule numbers ( simulation with many formamide molecules )

From: Adrien Delmont (adriendelmont_at_yahoo.com)
Date: Sat Jul 26 2008 - 10:55:11 CDT

  Dear Ross Walker, Thank you very much for your help and suggestions . But  I don¢t thing that I completely  understood  writing a quick shell script and the next steps that you explained. Could you please explain these jobs  in details? How can I prepare a quick shell script and how should  be the quick shell script¢s content?  Many thanks in advance   Adrien ----- Original Message ---- From: Ross Walker <ross_at_rosswalker.co.uk> To: amber_at_scripps.edu Sent: Saturday, July 26, 2008 4:58:34 PM Subject: RE: AMBER: big molecule numbers ( simulation with many formamide molecules ) Hi Adrien,   You can't directly define the number of molecules of formamide that solvatebox adds, just the buffer. However, it is fairly simple to write a quick shell script that runs tleap and refines the buffer size to the solvatebox command to give you the number of formamide molecules that you require.   If you want to see the formamide box after you solvated your solute just 'edit' the unit in xleap. Alternatively save your prmtop and inpcrd files and then look at them in something like VMD. The tutorials on the amber website show you how to do this.   Good luck, Ross   From:owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Adrien Delmont Sent: Saturday, July 26, 2008 2:04 AM To: amber_at_scripps.edu Subject: AMBER: big molecule numbers ( simulation with many formamide molecules )   Dear All,   Thanks a lot for your suggestions. I want to run a simulation with many formamide molecules. Well but How can I define the molecule number for a 'solvent' box containing lots of my own molecules. And Are there any different options for running a simulation with many formamide molecule ? also I want to see the simulation box and my formamide molecules in it. So How can I do that?   Many thanks in advance   Adrien

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