some recommendations for parametrizing new molecules required

From: CHINDEA Vlad (
Date: Fri Jan 23 2009 - 03:31:04 CST

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
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