AMBER Archive (2009)

Subject: Re: [AMBER] Strange contacts with water molecules

From: Jordan MONNET (
Date: Tue Jun 09 2009 - 11:01:53 CDT

Dear Ross,

> This does look pretty weird. Do you have the prmtop and original
> inpcrd
> file? Plus the restart file produced by the run? This looks to me
> like there
> must be some issue with the initial structure

I do and it looks ok.

> If you watch the trajectory file can you see where things start going
> weird?

I am not sure but it seems to become weird with the production process

> ndfmin and ntcm are 'very' deprecated. I have to go back to AMBER
> v7.0 to
> even find a description in the manual

As you well noticed, I updated AMBER 7 to AMBER 10 but I did the
protocol with AMBER 7 manual...

Thank you so much, I will look into my input file and make it better !
I guess it
will make this strange problem disappear

Jordan MONNET (3rd grade student)
Bachelor in Biology & Computer science
University of Paris Diderot (Paris VII)
Phone: +336 20 70 24 93

" The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...' " Isaac Asimov

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