Re: some recommendations for parametrizing new molecules required

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jan 23 2009 - 11:17:09 CST

One thing you might consider: if you have access to a supercomputing
center, they may have Gaussian installed. I know, for example, the
Pittsburgh Supercomputing Center has it, and I think NCSA does as well.

On Jan 23, 2009, at 3:31 AM, CHINDEA Vlad wrote:

> Dear NAMD users
>
> At this moment I am pondering on the strategy I will follow in
> order to parametrize for NAMD a drug molecule with 124 atoms. It is
> quite a complex tricyclic molecule, not baring much resemblance
> with molecules already parametrized. I have read the Paratool
> guideline and the additional information from Mackerell and now I
> would need some clarifications before starting:
>
> I seems quite possible that I will not get Gaussian through our
> university which means that I will have to use other programs. In
> Paratool tutorial it is stated that GAMESS could be used but there
> is not much information given on how to proceed with it. Before
> embarking on using this program I would need reassurance that it is
> indeed possible to use GAMESS for this purpose (is there maybe some
> progress on developing Paratool compatibility with GAMESS ?) and
> maybe some pointers on the differences between using Gaussian and
> GAMESS (I am guessing at least the manual input of the QM results
> from GAMESS in Paratool).
>
> Which of the 3 GAMESS (US, UK, PC/Firefly) to use ? Important
> criteria here would be speed, availability of support and previous
> work done with any of these programs for preparing NAMD input. I
> have checked a little bit all programs and I only found a limited
> number of benchmarks which are favorable to PC/Firefly. So what is
> your opinion here ?
>
> I would appreciate a rough idea on the computation resources
> required. As my molecules splits naturally by cycles and the
> largest of them has about 80 atoms it seems to me that this will be
> the largest fragment on which I will have to do single-point QM. Is
> this reasonable to calculate on a single Intel P4 2,66 Ghz
> processor at the required level of theory ? As I understand the
> threshold for such calculations is usually 120 atoms, but with what
> computational power ? I could live with calculations taking days,
> but not weeks !
>
> Is there a difference in using CHARMM or AMBER charges ? I
> understand that they are calculated differently but once calculate
> does NAMD cares about this distinction (as it does for example for
> parameters file format: either CHARMM or X-PLOR) ? Or is there any
> limitation in using one or the other ?
>
> Sorry for the long mail and thank you for your support
>
> All the best !
>
> Vlad Chindea
>
> What can you do with the new Windows Live? Find out

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