[AMBER] query with multocomponent system

From: kaustubh joshi <kandrjoshi.gmail.com>
Date: Tue, 28 Jun 2011 16:49:29 +0200

Hello,
 I was following link to work for a system with more than one molecule.
http://archive.ambermd.org/201009/0664.html

I have to generate system with a simple nitrile and amine molecule.

I am following the procedure given below:

My suggestion is to take each separate small
molecule<http://archive.ambermd.org/201009/0651.html#>,
parameterize it using
antechamber (I used) if that works for you (maybe use R.E.D. if you need
more
stringent charge derivation), then load it into leap and use the "saveoff"
procedure to save an amber library file. For example, suppose you have 2
small molecules molecule1.pdb and molecule2.pdb. Use R.E.D. or antechamber
as you will, and get the files molecule1.mol2 and molecule2.mol2 with
partial charges for each atom. Then load them into leap as such:

mol1 = loadmol2 molecule1.mol2
mol2 = loadmol2 molecule2.mol2

saveoff mol1 Molecules <http://archive.ambermd.org/201009/0651.html#>.lib
saveoff mol2 Molecules.lib

This will create a library file "Molecules.lib" that has all of the bonding
and charge information for each of your molecules. Then you can use packmol
to create your combined PDB file, which should have the molecules in
Molecules.lib each with the same residue name and atom names. Then, you can
load this library into leap:

loadoff Molecules.lib

total_mol = loadPDB packmol_structure.pdb

And then you just have to make sure that you have parameters for all of the
atom types and bonds/angles/dihedrals. You can use parmchk on each of the
original mol2 files to get these.

Hope this helps,
Jason
------------------------
I generated the Molecule.lib with information for the 2 molecules.
I also made a pdb file containing the nitrile and amine molecule's details
obtained from the same pdb files for amine and nitrile used to generate the
lib file.
But I am slightly confused with your words saying "Then you can use packmol
to create your combined PDB file, which should have the molecules in
Molecules.lib each with the same *residue name and atom names*."
What exactly the bold letters mean.
---------------------------------------
While I try to load the pdb file I end with message:
total=loadpdb molecule2.pdb
Loading PDB file: ./molecule2.pdb
Unknown residue: MTL number: 0 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: NIL number: 1 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: MTL number: 2 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
  -no luck
Unknown residue: AMN number: 3 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: MTL sequence: 1
Created a new atom named: C1 within residue: .R<MTL 1>
Created a new atom named: H12 within residue: .R<MTL 1>
Created a new atom named: H13 within residue: .R<MTL 1>
Created a new atom named: H14 within residue: .R<MTL 1>
Creating new UNIT for residue: NIL sequence: 2
Created a new atom named: N within residue: .R<NIL 2>
Created a new atom named: C within residue: .R<NIL 2>
Creating new UNIT for residue: MTL sequence: 3
Created a new atom named: C1 within residue: .R<MTL 3>
Created a new atom named: H12 within residue: .R<MTL 3>
Created a new atom named: H13 within residue: .R<MTL 3>
Created a new atom named: H14 within residue: .R<MTL 3>
Creating new UNIT for residue: AMN sequence: 4
Created a new atom named: N1 within residue: .R<AMN 4>
Created a new atom named: H11 within residue: .R<AMN 4>
Created a new atom named: H12 within residue: .R<AMN 4>
  total atoms in file: 13
  The file contained 13 atoms not in residue templates
----------------------------------------
I don't understand how to proceed.
I am attaching the generated pdb and the lib file.Kindly help me.

Can not attach lib file, attching its data in word format:

Kaustubh


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Received on Tue Jun 28 2011 - 08:00:06 PDT
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