AMBER Archive (2006)

Subject: AMBER:

From: uccadco_at_ucl.ac.uk
Date: Tue Nov 28 2006 - 08:48:08 CST

Hello all,

I am starting with AMBER, i am using AMBER 8.0 Introductry Tutorial, so I have
download 1npo.pdb file, I have deleted A, C and D chains, save my file as
oxyt.pdb. Now, i opened the file with spdbv and i saved it as oxyt_np.pdb.
I opened xleap:
xleap -s -f leaprc.ff03
into xleap:

> oxy = loadPdb oxyt3_np.pdb
Loading PDB file: ./oxyt3_np.pdb
  Added missing heavy atom: .R<CGLY 9>.A<OXT 8>
  total atoms in file: 68
  Leap added 68 missing atoms according to residue templates:
       1 Heavy
       67 H / lone pairs
> bond oxy.1.SG oxy.6.SG
> check oxy
Checking 'oxy'....
Warning: Close contact of 1.831870 angstroms between .R<ASN 5>.A<H 2> and .R<CYS
6>.A<H 2>
Checking parameters for unit 'oxy'.
Checking for bond parameters.
Could not find bond parameter for: SH - SH
Checking for angle parameters.
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
There are missing parameters.
check: Warnings: 1
Unit is OK.

When I tried save topology and coordinate files program did not it.

Can somebody help me?
Sorry if I am not enough clear, my english is not very good.

Thanks in advance.
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