AMBER Archive (2002)

Subject: again...Minimization of pentane holding a plane of carbon atoms

From: Hungie Hungie (hungie01_at_hotmail.com)
Date: Wed Apr 17 2002 - 13:03:23 CDT

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Dear Amber's users,

According to my previous message, I also have quesions.

1. Can I use parameters in parm94.dat with pentane?
My purpose is to minimize organic compound using force field level comparing
with other level.
2. My PDB file contains

ATOM 1 C UNK 1 0.000 0.000 0.000 1.00 0.00
ATOM 2 H UNK 1 -0.900 0.632 0.000 1.00 0.00
ATOM 3 H UNK 1 -0.900 -0.632 0.000 1.00 0.00
.
.
.

When I load PDB using tleap, I obtained message below
-----------------
>aa = loadpdb pentane.pdb
Loading PDB file: ./pentane.pdb
-- residue 1: duplicate C atoms (total 5)
-- residue 1: duplicate H atoms (total 12)

   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

Unknown residue: UNK number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
Creating new UNIT for residue: UNK sequence: 1
Created a new atom named: C within residue: .R<UNK 1>
Created a new atom named: H within residue: .R<UNK 1>
  total atoms in file: 17
  The file contained 2 atoms not in residue templates
>
-------

I can't save parmtop and inpcrd files.

Could you please give me any suggestion?

Thank you very much inadvance for your help.

Hungie

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