AMBER Archive (2004)

Subject: RE: AMBER: problem loading pdb in leap.

From: Andrew Box (
Date: Tue Aug 24 2004 - 01:30:46 CDT

I found that you needed to run the pdb structures form insight through
Antechamber (see manual for commands) to generate a .prepin file and a
frcmod file. These can then be read into amber and saved successfully.


>From: <>
>To: amber mail reflector <>
>Subject: AMBER: problem loading pdb in leap.
>Date: Tue, 24 Aug 2004 09:52:05 -0500 (GMT)
>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
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