When attempting to run "loadmol2" on my mol2 file (attached), I get the following error:
"Fatal Error: last line read: 1 C1 -0.3770 0.4960 -1.4850 c 1 0.816500"
This was after my parmchk returned a "memory allocation error", and I skipped that step because my frcmod file came back clean.
Does anyone know what may have caused this?
Clayton Buback
Chemical Engineering with a Biochemical Emphasis,
Missouri University of Science & Technology
President, International Society for Pharmaceutical Engineering
Secretary, Scrubs Pre-Health Society
Public Relations Coordinator, International Students Club
Pledge Education Teaching Assistant, Alpha Chi Sigma
cbnf6.mail.mst.edu
(314)584-0002
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Thursday, September 20, 2012 7:54 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Antechamber
On Tue, Sep 18, 2012, Buback, Clayton (S&T-Student) wrote:
>
> On Wed, Sep 12, 2012, Buback, Clayton (S&T-Student) wrote:
> >
> > I am trying to run a novel, non-biomolecule system containing 72
> > atoms. Following the Antechamber tutorial, I have successfully created
> > a mol2 file. However, when I run the parmchk command, it returns this
> > error:
> >
> > "Memory allocation error on *atom"
Works for me; what version of AmberTools are you using? What compiler and OS?
FWIW, parmchk returns any empty frcmod file, meaning that all the needed
parameters are already in gaff.dat. So, as a workaround, you can just skip
the parmchk step.
....dac
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- application/octet-stream attachment: Core.mol2
Received on Wed Sep 26 2012 - 12:30:03 PDT
