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.cgl.ucsf.edu>
To: amber.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.cgl.ucsf.edu>
To: amber.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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Received on Sun Apr 12 2009 - 01:09:33 PDT
