Re: [AMBER] sqm x mopac in AmberTools 1.3

From: Alan <>
Date: Tue, 29 Dec 2009 18:49:26 +0000

Dear Prof. David,

I tried to modify line 555 in amber11/src/antechamber/charge.c to :


recompiled everything again, and tested, but no file 'sqm.pdb' showed up.

Is there something else I can do?

Thinking aloud, I am afraid that routine 'wpdb_optimized' may not know well
what to do with 'sqm.out' file due to its format, could it be that?

Many thanks in advance,


On Wed, Dec 23, 2009 at 03:50, David A. Case <>wrote:

> The final coordinates are in the sqm.out file. You could also uncomment
> line 555 in amber11/src/antechamber/charge.c, to have antechamber write
> the optimized coordinates as it has done with mopac.

Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
AMBER mailing list
Received on Tue Dec 29 2009 - 11:00:02 PST
Custom Search