AMBER Archive (2006)

Subject: AMBER: Pt containing complex: xleap

From: a a (patd_2_at_hotmail.com)
Date: Sun May 28 2006 - 22:30:48 CDT

Dear Sir/Madam,

I am trying to do an MD calculation for Pt containing inorganic complex. I
tried to edit the pdb file as nuc.pdb in tutorial one. but when I tried to
open the file with xleap, the following message occur

"Unknown residue: MOL number: 0 type: terminal/last .. relaxing and
constraints to try for a dbase match no luck
Creating a new UNIT for residue: MOL sequence: 1
Created a new atom named: PT1 within residue: R < MOl 1>
Created a new atom named: N1 within residue: R< Mol1>
........
total atoms in file: 39
The file contained 39 atoms not in residue templates"

When I type edit filename, I see all the atoms in the right positions but no
connections between them in the picture. I think it is a wrong way of doing
this calculations for Pt containing complexes.

Could you please kindly give me a hand to teach me how to do it correctly?

Best regards,

aa

_________________________________________________________________
Get 10Mb extra storage for MSN Hotmail. Subscribe Now!
http://join.msn.com/?pgmarket=en-hk

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu