From: zoran (
Date: Tue Dec 16 2014 - 09:42:00 CST

Hi Francesco,
Unfortunately I cannot help as I am working now on better psf/pdb files so may be Chris could give you an adequate reply. btw I attached the complex anion which I intent to link with DNA dodecamer.


From: Francesco Pietra
Sent: Tuesday, December 16, 2014 8:21 AM
To: zoran
Cc: VMD Mailing List ; Christopher Mayne ; Josh Vermaas ; Axel Kohlmeyer
Subject: vmd-l: Re: FFTK work's with molecules containing new atom types

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.



On Tue, Dec 16, 2014 at 12:57 AM, zoran <> 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.