Hi all amber users,
I used RESP charges from RED to generate the parameters for an organic
molecule. I have to substitute some of the aminoacids in a protein by this
residue. For this I use Insight II where I manually delete the orignal
aminoacid and then attach this residue and then save the pdb file.
After loading the frcmod and prepin files for this ligand in xleap, I load
my modified protein. when there is a single aminoacid substitution, it
loads it properly without any error but when i try to load the pdb file
with more than 1 substituted amonoacids, leap gives the error:
>loadamberparams lyk.frcmod
Loading parameters: ./lyk.frcmod Reading force
field mod type file (frcmod)
> loadamberprep lyk_resp3.prepin
> q=loadpdb bsa-mod2.pdb
Loading PDB file: ./bsa-mod2.pdb
-- residue 597: duplicate [ C1] atoms (total 2)
-- residue 597: duplicate [ C10] atoms (total 2)
-- residue 597: duplicate [ C13] atoms (total 2)
-- residue 597: duplicate [ C14] atoms (total 2)
-- residue 597: duplicate [ C15] atoms (total 2)
-- residue 597: duplicate [ C16] atoms (total 2)
-- residue 597: duplicate [ C17] atoms (total 2)
-- residue 597: duplicate [ C18] atoms (total 2)
-- residue 597: duplicate [ C27] atoms (total 2)
-- residue 597: duplicate [ C28] atoms (total 2)
-- residue 597: duplicate [ C29] atoms (total 2)
-- residue 597: duplicate [ C3] atoms (total 2)
-- residue 597: duplicate [ C31] atoms (total 2)
-- residue 597: duplicate [ C32] atoms (total 2)
-- residue 597: duplicate [ C5] atoms (total 2)
-- residue 597: duplicate [ C8] atoms (total 2)
-- residue 597: duplicate [ C9] atoms (total 2)
-- residue 597: duplicate [ H12] atoms (total 2)
ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
(same-name atoms are reduced to a single atom)
Created a new atom named: H within residue: .R<NTHR 1>
Created a new atom named: HD1 within residue: .R<PRO 112>
Created a new atom named: HG1 within residue: .R<PRO 112>
Created a new atom named: HB1 within residue: .R<PRO 112>
Created a new atom named: HB1 within residue: .R<LEU 113>
Created a new atom named: HB1 within residue: .R<GLU 393>
Created a new atom named: HG1 within residue: .R<GLU 393>
Created a new atom named: HB1 within residue: .R<LEU 394>
Created a new atom named: OXT within residue: .R<ALA 580>
One sided connection. Residue: IB missing connect0 atom.
One sided connection. Residue: missing connect1 atom.
Created a new atom named: H2 within residue: .R<lyk 597>
Created a new atom named: H4 within residue: .R<lyk 597>
Created a new atom named: H6 within residue: .R<lyk 597>
SAME MESSAGE FOR ALL THE lyk RESIDUES (SUBSTITUTED ONES)
total atoms in file: 9293
Leap added 39 missing atoms according to residue templates:
35 H / lone pairs
4 unknown element
The file contained 41 atoms not in residue templates
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I am working on amber 7. Can anyone tell where I am going wrong and what I
need to rectify this oriblem. I would also like to know if there is any
method (in amber 7 or 8 or any where else) by which I can easily replace
the standard aminoacid by the new ligand?
Any sort of advise and suggestion will be of great use.
with regards
Anshul Awasthi
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India.
Mobile +91-9872220352
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Received on Sat Jul 24 2004 - 06:53:00 PDT
