Re: [AMBER] Add residue from PDB file

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Sat, 9 Jan 2010 18:39:44 -0600

Dear Xihui, from a previous Amber list post...
____________________________
It seems obvious after you know how....here is a typical tleap workflow:

source leaprc.ff99SB (for the protein part)
source leaprc.gaff (for the ligand part)
loadMol2 ligand.mol2 (where ligand.mol2 is created by antechamber) OR
loadAmberPrep ligand.prepi (where ligand.prepi is created by antechamber)
loadAmberParams frcmod (to get ligand-specific parameters, if any, created
                           by parmchk)

complex = loadPDB complex.pdb (where complex.pdb has consistent coordinates
                               of both the protein and the ligand, with the
                               ligand residue and atom names the same as in
                               the mol2 or prepi files loaded above. You
                               should have a TER card separating protein and
                               ligand.)

...solvate, etc.
saveAmberParm complex complex.top complex.crd
quit

Note that Amber does not create the complex.pdb file -- you get that from
a docking program, or from the PDB, or from wherever. LEaP will use
whatever
coordinates are in that file, so check things visually before proceeding.
_________________________________________________________
Hope this helps
Dean

-- 
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
> From: Xihui Yin <xihui1010.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Sat, 9 Jan 2010 02:08:45 -0600
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Add residue from PDB file
> 
> Hi Amber users,
> 
> I want to simulate the interaction of two molecules which come from one PDB
> file, but I don't how to add two residues into one unit. I thought maybe I
> should use the command "add" , however, it doesn't work.
> 
> Following is what I've done (doesn't work)
> 
>> MOL = loadpdb molecule.pdb
> (C6 is the residue name of the molecule)
>> a = copy MOL
>> add a C6
> 
> Does any one know how to do it? Thanks a lot.
> 
> Best,
> Xihui
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> AMBER mailing list
> AMBER.ambermd.org
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Received on Sat Jan 09 2010 - 17:00:02 PST