pentane minimization

From: Hungie Hungie <>
Date: Thu 18 Apr 2002 16:15:33 +0700

Dear All,

Thanks for suggestions of Bill Ross, X. Tan, and Eva Darian. However, I am
still confused. I have run minimization and MD for DNA duplex (using Amber6)
which I did't need extra force field and template of molecule. I have had a
look in tutorial for Biotin which for extra force field and individual
charge for each atom.

For pentane, I would like to minimize structure. I have *ONLY* PDB file as
ATOM 1 C1 PEN 1 0.000 0.000 2.400 1.00 0.00
ATOM 2 1H1 PEN 1 0.600 0.000 3.400 1.00 0.00
ATOM 3 2H1 PEN 1 -0.900 0.632 2.400 1.00 0.00

Could you please tell me?
1. Can I use force field of parm94.dat? I have no extra force field and
charge for each atom.
2. I tried to SaveAmberParm using tleap after loadpdb, I can't save.

>aa = loadpdb pentane.pdb
Loading PDB file: ./pentane.pdb
Unknown residue: PEN number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: PEN sequence: 1
Created a new atom named: C1 within residue: .R<PEN 1>
Created a new atom named: H11 within residue: .R<PEN 1
  total atoms in file: 17
  The file contained 17 atoms not in residue templates
>saveamberparm aa pen.prmtop pen.inpcrd
Checking Unit.
FATAL: Atom .R<PEN 1>.A<C1 1> does not have a type.
FATAL: Atom .R<PEN 1>.A<H11 2> does not have a type.
Failed to generate parameters
Parameter file was not saved.

3. DO I need to build template for pentane? how? I have no any charge for
each atom.

Thank you very much for your kindness in advance.


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Received on Thu Apr 18 2002 - 02:15:33 PDT
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