AMBER Archive (2009)

Subject: Re: [AMBER] Topology Reorder for EVB

From: Andrea Coletta (a.coletta_at_caspur.it)
Date: Tue Dec 08 2009 - 03:40:23 CST

Jason Swails ha scritto:
> As far as I know, antechamber should be able to create mol2 files just fine
> (I've done it on several occasions). There may be some kind of error on the
> antechamber system call perhaps? What command are you using to execute
> antechamber? (I've likewise been able to use babel to produce mol2 files,
> which command are you using for that as well?)
>
there was a compilation problem, or a library missing i don't know, but
i've tried on another machine and it works.
> Another way you may try doing this with an amber prep file is to save it as
> a cartesian prep file (prepc instead of prepi). In this case, the residue
> is not stored as a zmat so the order of the atoms no longer matters. Thus,
> you may be able to reorder the prep files to match just by swapping lines.
>
it's was i was trying to do, but isn't so easy!
Have you noticed the fourth column in the prep section where the atoms
type and positions are defined?
That one full of "M","E","S","B" or "[1234]" ?
That's the real issue, because it's a local definition of the topology
(see http://ambermd.org/doc/prep.html)
and changing the order you change the whole topology...
Anyway, the .mol2 thing worked... so problem solved

Thank you all

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