AMBER Archive (2009)

Subject: Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10

From: Keith Van Nostrand (kifvan_at_yahoo.com)
Date: Wed Jul 22 2009 - 10:58:08 CDT

Dr. Walker,     I have attached a .tar of the files needed to attempt my calculation.   Here is my procedure:   1.  First I cat together 15 reactant and 15 product inpcrd files for coordinate input for addles.  I used the cat-reactant15X-product15X.bat file to do this with reactant.inpcrd and product.inpcrd.   2.  I run addles with the addles.in file as follows:   addles < addles.in > addles.out   3.  I then use 30image-neb-4proc.bat to run sander.MPI on a linux cluster machine.     Let me know if anything sticks out.  Thank you very much for your help.   Sincerely, Keith Van Nostrand   ________________________________ From: Ross Walker <ross_at_rosswalker.co.uk> To: AMBER Mailing List <amber_at_ambermd.org> Sent: Thursday, July 16, 2009 11:34:13 PM Subject: RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Hi Keith, >  I have double checked that I am using the addles that came with Amber > 10.  A fresh checkout of Amber 10 was done yesterday and recompiled > with the same results. >  I notice that the top of the addles output says: > >  AMBER8 Module: addles >  set up Locally Enhanced Sampling topology I suspect this was just overlooked when the code was updated and you have the AMBER 10 version. Can you possibly send me the files you are using to set this up along with the instructions for how you are doing it so I can try it out myself and check what you are trying? All the best Ross /\ \/ |\oss Walker | Assistant Research Professor | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.  _______________________________________________ AMBER mailing list AMBER_at_ambermd.org http://lists.ambermd.org/mailman/listinfo/amber


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