VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Feb 29 2012 - 05:52:03 CST

I would like to try FFTK to parameterize a simple complex of a
transition metal. How to setup the "Input PSF File"? Perhaps my
attempt through the autoPSF plugin is not the right way as, obviously,
it fails to provide the desired file.

thanks

francesco pietra

On Sat, Feb 18, 2012 at 11:39 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> I will add that this is similar to what I did for an Fe ion coordinated by a
> protein.  Obviously you won’t learn anything about binding/unbinding, but it
> should at least represent the bound state reasonably well, vs. the
> alternative of having the ion free (which may be interesting to look at for
> comparison anyway).  One additional note though: I had to create some new
> atom types for coordinating residues in order to have unique parameters for
> all the bonds/angles/dihedrals.  Then I had to copy existing protein
> parameters for those types to the new ones.
>
>
>
>
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Mayne, Christopher G
> Sent: Saturday, February 18, 2012 3:40 PM
> To: chiendarret_at_gmail.com
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Re: About FFTP with transition metal complexes
>
>
>
> Francesco,
>
>
>
> FFTK was designed primarily with small molecule organics in mind.  I am not
> familiar with the specifics of parameterizing metal complexes for CHARMM;
> however, if it follows the same (or similar) workflow as organics, then FFTK
> should, in principle, be applicable/useful.
>
>
>
> To answer your questions directly:
>
>
>
> 1) FFTK relies heavily on QMtool for parsing Gaussian log files within the
> charge optimization routine.  Try loading the DFT calculation log file into
> VMD using QMtool; if the optimization steps are properly loaded and you can
> see step energies pushed to the TkConsole during the load, then it *should*
> work in FFTK.
>
>
>
> Note 1: you can still use FFTK to setup the calculation by changing the
> Route details with in the "Gaussian Setting" section using the appropriate
> Gaussian keywords
>
> Note 2: make sure that you calculate separate single point energies for the
> metal complex and a TIP3P water molecule at the same level of theory as used
> in the water interaction calculation.
>
>
>
> 2) This is a more of a general psf/topology question and not directly an
> FFTK question.  Since I don't work with metalloproteins, I'm only guessing
> here; hopefully someone else will chime in.
>
> You should be able to leave all topologies in tact and write a patch to
> adjust the partial charges for the ligating residues in addition to adding
> bonds/angles/dihedrals necessary to describe the ligated complex.
>
>
>
>
>
> Chris
>
>
>
>
>
> Date: Sat, 18 Feb 2012 07:23:01 +0100
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Subject: vmd-l: About FFTP with transition metal complexes
>
> My aim is to parameterize a transition metal complex for a
> metalloproteins. Two questions about FFTP, a most waited tool which
> going to foster a lot of research work.
>
> (1) Calculation of partial charges. When a transition metal is
> involved, a single-point HF would be inappropriate. Current literature
> about any type of dealing with such complexes suggests to go on - from
> beginning to end - with DFT, with higher basis set for the metal or
> metal ion. Who has specific experience for CHARMM ff to this regard.
> In any case, is FFTP prepared to accept the results (partial charges,
> geom data, force constants) from a DFT type of calculation? If so I
> could try to apply the plugin to my case.
>
> (2) As there is no tutorial yet for FFTP, it is not yet clear to me
> how to bind the parameterized metal complex to its protein. I make an
> example: for a metal ion bound to HIS and ASP residues, I make a model
> including a portion only of the HIS and ASP residues, while carrying
> out partial charge and bond data (geometry and force constants) for
> that model. Correspondingly, I have a protein from which the portion
> included into the metal complex has been removed. What about the
> procedure to establish chemical bonds between the abridged protein and
> the metal complex? (i.e., the equivalent of the command "bond xxx
> yyy" with Amber's LEaP).
>
> Thanks
> francesco pietra