VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Dec 16 2014 - 01:21:43 CST

Zoran, Christopher:

As I have missed some message, could you please let us know which metal
complex was parameterized (even without details if it is private work) and
along which lines? In particular, how were the bond and angle forces with
the metal (I assume that diedr forces are at < kT) extracted from the
(Cartesian, I imagine) matrix? amber uses either the Seminario (Cartesian
matrix) or Z-matrix method and I don't know how sound science is in those
methods because of the coupling between the various bond/angle motions.

I believe that it is high time that psfgen is accompanied by some tool for
transition metal complexes, like amber did (although in the limit of usage
that I illustrated before). Paratool was initiated but the founder left and
the plugin remained unusable. psfgen has huge advantage over amber, were
leap has so an intricate and fragmentary language to require abandoning
science to become an expert in such intricacies. Also, anyone that has
worked with leap for multichain systems knows how difficult is knowing were
one is.

thanks
francesco

On Tue, Dec 16, 2014 at 12:57 AM, zoran <zmatovic_at_kg.ac.rs> wrote:
>
>
> VMD people,
>
> Christopher just wrote that he succeeded to parameterize bonded parameters
> of my metal-complex. I am very happy because of this fact. This give me a
> chance to do the same (I hope) and finally to see is it classical ff
> really so bad for MD with TM (in geometry and energetic issues). This open
> to me more accurate door for other calc. (QM/MM for example).
>
> Once again thanks for all advices and critics from the members of this
> forum. Excuses for Christopher again.
>
> Cheers
> Zoran
>