On Fri, Jul 19, 2002, Salinthip Thipayang wrote:
> I am trying to change an amino acid residue in the active site of a protein
> The next step is to modify GLU in the active site to GLN and then compare the
> binding free energies.
>
> I am thinking of the following approaches.
>
> 1) Create the PDB file from the restart file obtained from the MD run using
> CARNAL
> 2) in XLEAP, loadpdb and then change the GLU264 to GLN 264
Much easier, I think: use a text editor to modify the pdb file to change GLU
to GLN,, change the atoms be what GLN would expect. Then use loadpdb to
read that into LEaP. And, use ambpdb to get the pdb file; this will ensure
that TER cards are placed between all of the waters. (That may have been
the origin of the "duplicate atoms" problem...it's hard to tell without more
information).
You will need to use a setBox command in leap to make sure the box info
is in the new prmtop file; get the box info from your last output, or from
the bottom of the restart file.
> 3) run belly MD first only allow the GLN264 to move and fix other residues and
> water and then run another belly MD allowing all the residues to move except
> the ligand so that the ligand can find the optimal structure with all the
> residues.
> 4) then run full MD for the whole system.
This sounds OK.
> >
> > > mutant2 = loadpdb "./mutantGLN_b4_xleap2.pdb"
> > Loading PDB file: ./mutantGLN_b4_xleap2.pdb
> > -- residue 10240: duplicate H1 atoms (total 10)
> > -- residue 10240: duplicate H2 atoms (total 10)
> > -- residue 10240: duplicate O atoms (total 10)
You should(?) be able to figure out what is going on by looking at the pdb
file. For some reason, LEaP thinks there are 10 H1 atoms in a single residue.
Make sure that the residue numbers are unique. Since you have more than
10000 residues, this may be a problem with residue numbering: check that
you don't have "*****" or somehting like that as a residue number in the
pdb file.
(Aside: I don't think your problem has anything to do with the fact that
GLN has more atoms than GLU).
(Another aside: depending on how detailed an answer you want, you might
consider the following: just "neutralize" the GLU by changing the charges
so they add up to zero for the residue, rather than to -1.) Then you don't
need to change anything except the few charges, which you could even do in
by hand in the prmtop file. This would capture to a large extent the
electrostatic change of this mutation; of course it would miss any details of
hydrogen bond donor properties of the NH2 group in GLN.)
..hope this helps....good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Fri Jul 19 2002 - 11:59:24 PDT
