AMBER Archive (2006)

Subject: AMBER: Trouble with combining a non-standard residue with a protein of standard residue

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Tue Mar 07 2006 - 15:21:44 CST

Dear amber users,
 I developed parameters for a non-standard residue (called CFP)
(formed by strange bonding of 3 standard residues) using antechamber.
During modeling, there were no terminal atoms (H and OH atoms). I put
it back in the protein (at position N) by first orienteering CFP such
that the atoms that should form bonds with N-1th and N+1th residues
are closest and then pasted the coordinates of CFP in the PDB file of
the protein. WHen i load this in xleap and say 'check UNIT', it forms
bonds between two distant atoms.

WARNING: There is a bond of 4.143970 angstroms between:
------- .R<PHE 63>.A<C 19> and .R<CFP 64>.A<OG1 1>
WARNING: There is a bond of 7.215575 angstroms between:
------- .R<CFP 64>.A<CD2 33> and .R<VAL 65>.A<N 1>

 I also discovered that it forms some other strange bonds too. Then I
used 'deleteBond' and "Bond' commands to make the right bonds:

deletebond t.63.C t.64.OG1
deletebond t.64.CD2 t.65.N
bond t.63.C t.64.N1
bond t.64.C3 t.65.N

And saved it as a PDB file. When I load this PDB file in Xleap, it
treat N+1th residue as a terminal residue and hence adds H atom to it.
It also gives the same error.

WARNING: There is a bond of 4.143970 angstroms between:
------- .R<PHE 63>.A<C 19> and .R<CFP 64>.A<OG1 1>
WARNING: There is a bond of 7.215575 angstroms between:
------- .R<CFP 64>.A<CD2 33> and .R<VAL 65>.A<N 1>

Why did it not save the changes that I made using bond and deletebond?

Also is there an easy way of seeing what bonds did amber make by itself?
What is the criteria for amber to make bonds between such distant atoms?

It there an easier way of doing combining this non-standard residue
with this protein? I have been working on it for two days and am at
the end of my wits?

thanks a lot in advance. Any help would be appreciated.
Rgds,
Nitin
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