VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Dec 16 2014 - 09:56:42 CST

Hi Zoran
When I set forth the difficulties in getting atrue QM minimum I had in mind
complexes of two transition metals with several aa carboxylates and
histidines. The one you show here should not present any difficulty in
getting a true QM minimum.

thanks
francesco

On Tue, Dec 16, 2014 at 4:42 PM, zoran <zmatovic_at_kg.ac.rs> wrote:
>
> 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.
>
> regards
> Zoran
>
>
>
> *From:* Francesco Pietra <chiendarret_at_gmail.com>
> *Sent:* Tuesday, December 16, 2014 8:21 AM
> *To:* zoran <zmatovic_at_kg.ac.rs>
> *Cc:* VMD Mailing List <vmd-l_at_ks.uiuc.edu> ; Christopher Mayne
> <mayne_at_ks.uiuc.edu> ; Josh Vermaas <vermaas2_at_illinois.edu> ; Axel
> Kohlmeyer <akohlmey_at_gmail.com>
> *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.
>
> 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
>>
>