AMBER Archive (2004)

Subject: AMBER: problem loading molecule in leap

From: anshul_at_imtech.res.in
Date: Thu Aug 26 2004 - 15:38:44 CDT

Dear amber users,
First of all I ould like to thank Ros to point out the mistake in my pdb
file. I was able to load the structure in leap after making the
corrections. Now I have 2 more questions:
1. I made the modifications to the protein structure by attaching an
organic molecule to an aminoacid residue in INSIGHT II. In the saved pdb
file the attached organic molecule is present in the end of the file as
the last residue. Now I load my prepin and frcmod files followed by this
molecule in leap and make proper bonds between the organic molecule and
the aminoacid. Now when I check this structure it shows a few warnings of
close contacts and an error:

Created a new atom named: OXT within residue: .R<ALA 582>

How to overcome this problem?

2. Next I tried to make modifications at 2 aminoacids. NOw when I tried to
load this structurte in leap, leap aborts with this error:

ERROR: Comparing atoms C15, H161, H162, H163 to atoms C15, O11, H161, H162
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 120 !FATAL: Message: Atom O11 is not
in the first list
!
!ABORTING.

Can anyone help me with these problems.
Thanks in advance

Regards,
Anshul Awasthi
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India.
Mobile +91-9872220352

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