AMBER Archive (2009)

Subject: Re: [AMBER] Sander and multiple residues

From: Dan Kaps (dan.kaps_at_yahoo.com)
Date: Fri Apr 10 2009 - 12:46:49 CDT

That is what I did. My problem is that i need .prmtop and .inpcrd files for both residues as they are in the .pdb file and I don't know how to do it. As far as I know the command is saveamberparm [unit] *.prmtop *.inpcrd where unit is the residue name. Since there are two residues it appears I can only get separate files. I tried using the leap function combine in order to combine the two residues into one...but thats where the overlap happened.
dan

________________________________
From: Bill Ross <ross_at_cgl.ucsf.edu>
To: amber_at_ambermd.org
Sent: Friday, April 10, 2009 12:42:36 PM
Subject: Re: [AMBER] Sander and multiple residues

> I did load the coordinates from a .pdb file...Do you have any suggestions
> for avoiding the overlap?

If loading from a pdb, how did you prepare the pdb? Did it have
all the atoms in it? Why did you use 'combine'?

Normally one prepares a pdb w/ the config one wants and loads it
as in the demos.

Bill

    
    ________________________________
    From: Bill Ross <ross_at_cgl.ucsf.edu>
    To: amber_at_ambermd.org
    Sent: Thursday, April 9, 2009 4:12:10 PM
    Subject: Re: [AMBER] Sander and multiple residues
    
    If you don't have a pdb file and choose to use 'combine', you
    have to be ready to select one of the units using xleap selection
    tools and drag/rotate it to where you need it.
    
    Ideally 'combine' would not overlap the units, but this is a hard
    problem - perhaps it could just create virtual boxes around them
    and use these to avoid overlap, issuing a warning to clean up the
    bond between the units. Note thatg leap minimization is useful but
    still does not take vdw into account, so overlaps are still an issue.
    
    Bill
    
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