Dear Dr Steinbrecher
Thanks alot for your kind suggestions. I will take care of the order of
common atoms in both input files. I will have identical starting coordinates
and they will appear in the same order.
But I am again confused in the tutorial at this paragraph.
"The first leap run (input file) will produce pdb files of the solvated und
neutralized benzene complex and of the benzene ligand in water (complex.pdb
and ligand.pdb). From these two additional pdb files are made by renaming
the BNZ molecule to PHN and deleting H6 (t4_phn.pdb and phn.pdb). These four
pdb files are then used in a second leap run (input file) to generate the
*.prm and *.rst files. This yields 4 parameter and 4 rst files."
Here you discussed that you are deleting H6 atom but not adding --OH at this
place in the files of complex having t4_lys bound with phenol (t4_phn.pdb
and phn.pdb). Is it the correct way ?? should also not add --CH3 in the
file, and just only delete --HO1 atom from :ROH.O1 ??
If i make the order of atoms in pdb file like --- Protein residues followed
by sugar atoms not in scmask fallowed by sugar atoms in scmask. I am not
solvating it twice all the water atoms have been kept in same coordinate
(as in your tutorial) after protein, sugar atoms without scmask and sugar
atoms with scmask. Is this order is ok to prepare prm and rst file with same
order of atoms ?
Thanking You
Sushil
rote:
> Hi,
>
> ok, it seems as if treating the whole sugar as one residue is not how your
> parameter files are set up. As I said, this should not be a problem for
> running your simulation. Unless you want to exercise how Amber residues
> are built and construct the sugars as single residues yourself, you will
> have to keep the setup as it is.
>
> Make sure about one thing though, namely that all atoms that are not in
> your scmask are in the same order in both prmtop files (they dont have to
> have the same atom numbers nor the same charges or names, but must appear
> in the same order). This is not automatically given for different
> molecules, unless someone built them specifically with Amber TI
> calculations in mind.
>
> Kind Regards,
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Fri Jan 15 2010 - 11:00:02 PST
