AMBER Archive (2003)

Subject: Re: AMBER: more than 100,000 atoms ?

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Thu Aug 07 2003 - 16:23:25 CDT

Dear David
I think you may be ok now. The next thing that breaks (If I recall
correctly) is the dihedral atom indexes. These for some historical reasons
get multiplied by 3. So, if any dihedral angle invloves an atom whose
atom number is larger than 33333 then the parm topology file gets screwed
up. The waters come after the solute (protein,dna etc.) so if these have
atom numbers below 33333, the waters won't mess you up--not having any
dihedrals.
Tom Darden

 On 7 Aug 2003, David Smith wrote:

> Hi all,
>
> Apologies if this question has come up before but I don't remember it
> and a quick search of the archives didn't net me anything.
>
> I wanted to try a system with more than 100,000 atoms. I know it's a bit
> big but my boss is an ambitious guy.....
>
> I gave it a go and initially got very confused by getting caught by
> "Peek Ewald" in a simple sander minimization.
>
> After a bit of surprise and a few write statements I realized that NATOM
> was being read as "I5" from the CRD file. Changing it to "I6" got me
> past "Peek Ewald" but I then got stuck a bit later. The web page tells
> me that, in general, NATOM is "I6" in PARMTOP but "I5" in CRD.
>
> I am still "trapped" in Amber 6 but my guess is that these formats
> persist into Amber 7 ?
>
> Can anyone recommend a way to do such a system with AMBER (any version)?
>
> i.e. Would I have to change all the formats associated with "read (9,F)"
> statements. Is there a semi fast way to do it ? Even if I did manage
> that, would the developers imagine that something else would break and
> that I should simply abandon the whole idea.
>
> Thanks for your patience ....
>
> David.
>
>
>

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