Dear Anshul
Can you post me your pdb file (as an attachment) please so that I can take a
look at it.
All the best
Ross
/\
\/
|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk/ | PGP Key available on request |
> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of anshul.imtech.res.in
> Sent: 24 August 2004 07:52
> To: amber mail reflector
> Subject: AMBER: problem loading pdb in leap.
>
> 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
>
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Received on Tue Aug 24 2004 - 06:53:00 PDT
