Quoting Nitin Bhardwaj <nbhardwaj.gmail.com>:
> I developed parameters for a non-standard residue (called CFP)
> (formed by strange bonding of 3 standard residues) using antechamber.
Do you mean there are three connections with other residues ?
In this case, if I remember you have to use a TER keyword in your PDB file...
> 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.
Did you set the head/tail of your residue (see LEaP manual)?
Moreover if you have a third connection, you could look at the CYX residue to
see and to set up the connections in this case.
> 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>
This is just a warning telling you that some bonds are too long in your residue.
My understanding of that is that it is unlikely your system (splited or not) has
been optimized by QM, but is manually adapted...
> 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
I can understand you need to create bonds between your residue and another one
belonging to your protein (like in the case of CYX) but I do not understand why
you need to remove bonds. This means to me that the topology of your molecule is
bad...
> 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.
Difficult to answer without the model...
> 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?
You could look at the CYX residue to understand how it is linked to three
residues. You could also look at R.E.DD.B. projects
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-1/leaprc-mol2tooff.ff
where you will find scripts which convert tripos mol2 files into OFF files:
This should help you to understand the "connections" between residues...
regards, Francois
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Received on Sun Mar 12 2006 - 06:10:17 PST
