AMBER Archive (2009)

Subject: Re: [AMBER] Sander and multiple residues

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Apr 10 2009 - 15:42:14 CDT

I am wondering whether you have taken a good look at the tutorials?

1. prepare pdb with all residues and correct atom names.
2. loadpdb
3. saveamberparm
4. run sander etc.

It is twice as simple as you seem to expect, and should be obvious
from the tutorials.

Bill

> My problem is that i need .prmtop and .inpcrd files for bot
> h residues as they are in the .pdb file and I don't know how to do it. As far a
> s 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 res
> idues into one...but thats where the overlap happened.

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