Dear Andrea,
> I created library files for a modified DNA residue using the RED 4
> program and Leap. The nucleoside worked just fine and was recognized by
> Leap. When I try to incorporate the nucleotide into a DNA strand, it
> fails.
1) I looked at your structure in the OFF file format.
Your deoxyribose is different from the canonical C2'endo & C3'endo
conformations... and your two aromatic cycles are quite distorted...
Did you try to optimize your structure using different initial
Cartesian coordinate sets ? do you reach always the same minimum ?
i.e. is your minimum representative ?
2) the atom names & residue name found in a FF library (mol2 file)
have to match those in the PDB file (containing the oligonucleotide)
> When I load my library file in leap, and type 'list' my residue
> (PAA) is present, and when I 'edit PAA' the residue appears as it
> should.
When I load your OFF in LEaP using:
PAA = loadoff PAA.lib
edit PAA
=> this does not work.
When I load your OFF in LEaP using:
QQQ = loadoff PAA.lib
edit PAA
=> this works - this is strange...
> When I load the pdb containing the residue, the program does not
> recognize any of the residues in the strand, even the unmodified ones
> ("The file contains 637 atoms not in residue templates"). But I can load
> the pdb file in VMD and it looks fine, except for close contacts between
> the modified base and nearby residues.
load mol2 file or prmtop/prmcrd files in VMD instead of PDB file so
that only real connectivities will be displayed
> Could the close contacts cause this problem?
No I do not think so.
Once you generated the central fragment in the mol2 file format for
your modified nucleotide using R.E.D.-III.4:
- check rigorously the atom names (Ante_R.E.D. 2.0 will solve many
problems here). Can leap differentiate H5'' from H5' ? I would check
that...
- add the FF atom types for the Cornell et al atom type
- define the head & the tail
See for instance
http://q4md-forcefieldtools.org/REDDB/projects/F-60/script1.ff
set PAA name "PAA"
set PAA head PAA.1.P
set PAA tail PAA.1.O3'
set PAA.1 connect0 PAA.1.P
set PAA.1 connect1 PAA.1.O3'
set PAA.1 restype nucleic
set PAA.1 name "PAA"
- load the PDB file of your oligonucleotide containing your PAA residue
=> the match has to work
- save the mol2 file of your oligonucleotide do display it in VMD
- save the prmtop/prmcrd of your oligonucleotide do display it in VMD
regards, Francois
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Received on Wed Oct 20 2010 - 08:30:03 PDT
