Re: [AMBER] antechamber

From: Alan <>
Date: Wed, 1 Jul 2009 12:37:40 +0100

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.)
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:

    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/
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.


On Wed, Jul 1, 2009 at 10:17, R. A.<> 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
> --
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Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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Received on Mon Jul 06 2009 - 12:26:59 PDT
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