AMBER Archive (2004)

Subject: AMBER: problem loading pdb in leap.

Date: Tue Aug 24 2004 - 09:52:05 CDT

Dear Amber users,
I am trying incorporate an organic molecule in my protein structure and
then analyse the effects.For this I generated the RESP charges and
parameters. I changesd my protein structure using INSIGHT II and tehn save
the structure as pdb to load in leap. Structure was saved without
hydrogens which will be added by leap. now when I load it in xleap it
loads it without any errors.

Loading PDB file: ./mod1.pdb
     total atoms in file: 4661
Leap added 4576 missing atoms according to residue templates:
     4576 H / lone pairs

But after this when i use the check command it gives a whole lot of
warnings regarding the unusual bonds and close contacts for every
residue.When i view the structure using edit command it shows a totaly
distorted structure, in the form of an extended rod. Along with these
warnings it also complains about the missing bond and angle parameters:

Checking parameters for unit 'x'.
Checking for bond parameters.
Could not find bond parameter for: o - N
Checking for angle parameters.
Could not find angle parameter: o - N - H
Could not find angle parameter: o - N - CT
Could not find angle parameter: c - o - N
There are missing parameters.
check: Warnings: 120937
Unit is OK.

However if iload the orignal protein ie without any modification it shows
it as the way it should be.

Can anyone tell what be going on here and how to overcome this. I am using
amber 8 on SGI orign.

Thanks in advanse for any kind of help and suggestions.

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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to