AMBER Archive (2002)

Subject: To PROFEC users

From: Salinthip Thipayang (salinthip.thipayang_at_ic.ac.uk)
Date: Fri Apr 19 2002 - 09:13:11 CDT

> Dear PROFEC users,
>
> I am trying to use PROFEC to
> qualitatively predict the
> effect of changing the
> residue in the binding site
> of a protein from the free
> energy calculations obtained
> from PROFEC. The first step
> of using PROFEC ( as I
> understand from the manual)
> is to make particle grids
> (van der Waals and
> electrostatic) for the
> protein-ligand and for
> ligand-water systems, using
> the makeGrid file (or
> profec_grid in AMBER6). The
> manual describes the command
> line as:
>
> cat <traj> | makeGrid <in>
> <top> <crd> <ljp> <vdw>
> <esp> <obj> <sav>
>
> I understand that cat <traj>
> is obtained from the mdcrd
> file as obtained by SANDER.
> makeGrid <in> is the input
> command file which is
> briefly described and an
> example is given in the
> manual. <top> is the AMBER
> topology file as obtained in
> Xleap. <crd> is the mdcrd
> file contained coordinate
> references and can be
> obtained by Xleap. But how
> and where can I obtain the
> <vdw>, <esp>, <obj> and
> <sav> files? What programs
> do I have to use to get
> them? The manual descibes
> what they are but does not
> say how are they calculated
> and what programs required
> to get these files to
> generate the grids. I notice
> the second step after the
> makeGrid process is the
> makeDiffGrid and we need to
> generate the <protein.vdw>,
> <solvent.vdw>, <output.vdw>,
> <protein.esp> etc. Anther
> obvious question is how can
> one generate these
> <protein.vdw>,
> <solvent.vdw>?
>
> I have read the quoted
> references about PROFEC e.g.
> from
>
> R.J.Radmer and P.A.Kollman,
> 'The application of three
> approximate free energy
> calculations methods to
> structure based ligand
> design: Trypsin and its
> complex with inhibitors', J.
> Computer-Aided Mol. Design,
> 12: 215-227, 1998.
>
> L.Wang et.al., 'Can one
> predict protein stability?
> An attempt to do so for
> Residue 133 of T4 Lysozyme
> using a combination of free
> energy derivatives, PROFEC,
> and free energy perturbation
> methods', Proteins:
> Structure, Function and
> Genetics 32: 438-458, 1998.
>
> M.A.L.Eriksson et.al.,
> 'Prediction of the binding
> free energies of new
> TIBO-like HIV-1 reverse
> transcriptase inhibitors
> using a combination of
> PROFEC, PB/SA, CMC/MD, and
> free energy calculation', J.
> Med. Chem., 42: 868-881,
> 1999
>
> These references are very
> useful but they do not
> describe the methods of
> using PROFEC in terms of the
> computational set up
> details. If there are any
> other references that you
> think may be useful, please
> quote them as well.
>
> Any comments, any
> recommendation will be
> greatly appreciated. Thank
> you everyone in advance for
> spending time reading/
> replying this email.
>
> I really hope to get some
> reply please!
>
> Yours sincerely,
>
> Salinthip Thipayang
> I
>
> --
> -------------------------------------------------------------------------------
> Salinthip Thipayang (Miss)
>
> PhD Research Student
> Biological and Biophysical Chemistry Research Group
> Chemistry Department
> Imperial College of Science, Technology and Medicine
> Exhibition Road
> London SW7 2AY
> The United Kingdom
> Tel: +44(0)207 5945851
> Fax: +44(0)207 5945845
> Email: salinthip.thipayang_at_ic.ac.uk
> --------------------------------------------------------------------------------
>
> 

--
-------------------------------------------------------------------------------
Salinthip Thipayang (Miss)

PhD Research Student
Biological and Biophysical Chemistry Research Group
Chemistry Department
Imperial College of Science, Technology and Medicine
Exhibition Road
London SW7 2AY
The United Kingdom
Tel: +44(0)207 5945851
Fax: +44(0)207 5945845
Email: salinthip.thipayang_at_ic.ac.uk
--------------------------------------------------------------------------------