AMBER Archive (2009)

Subject: Re: [AMBER] antechamber

From: gilbert_at_bluemarble.net
Date: Wed Jul 01 2009 - 07:11:17 CDT

  The version of Mopac6 that comes with antechamber is dimensioned for 100 heavy
(non hydrogen) atoms and 100 hydrogen atoms. The code is Fortran and there is no
dynamic memory allocation so this is a hard limit. If you want to run larger
systems you would need to change the parameters in the SIZES file and recompile.

Kevin

Quoting Alan <alanwilter_at_gmail.com>:

> I didn't even tried antechamber yet, but using my script to check your
> pdb and it failed:
>
> ERROR: Atoms TOO close (< 0.5 Ang.)
> ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Dist (Ang.) Atoms
> 0.32863 ['HETATM 131 H20 '] ['HETATM 201 H86 ']
>
> Check your pdb.
>
> I do use Pymol too, but I suggest you to do something like, in pymol
> terminal:
>
> cmd.sculpt_activate('t80p')
> for n in range(100): cmd.sculpt_iterate('t80p')
>
> this helps to relax your structure.
>
> Anyway, even doing that antechamber didn't run here:
>
> Total number of electrons: 716; net charge: 0
>
> Running: /Users/alan/Programmes/amber10/bin/mopac.sh
> Error: unable to find mopac charges in mopac.out
>
> Is net charge 0?
>
> And yes, your system is bigger than recommended (although sometimes I
> got topol for systems at that size). Maybe you should split it in 2.
>
> Cheers,
> Alan
>
>
> On Wed, Jul 1, 2009 at 10:17, R. A.<rabedi72_at_mail.com> wrote:
> > Dear Users
> >
> > I used pymol for creating my pdb structure and send it to antechamber for
> > creating prepin file.
> > Later I chacked out this file for any correction of atom type regarding
> > to gaff force field.
> > after running parmchk I got the error of ATTN, need revision. Also I
> > tried to load prepin in
> > xleap but I got the entry of type Dummy, atom H10 and also atom C44 not
> > created.
> > I checked everything related to this errors from archive and tried to fix
> > the things based on
> > suggestions and comments but the problem still continues. it seems my
> > structure is big for this
> > calculation as I found from the remarks?!. Any suggestions or comments
> > would be grateful. Thank you so
> > much in advance.
> >
> > Regards
> > RAK
> >
> > --
> > Be Yourself @ mail.com!
> > Choose From 200+ Email Addresses
> > Get a Free Account at www.mail.com
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber