Re: [AMBER] sleap never worked anymore since AT 1.2

From: David A Case <>
Date: Tue, 21 Jun 2011 09:26:13 -0400

On Fri, Jun 17, 2011, Alan wrote:
> sleap -f
> Warning: cannot find template for residue DMP in our library.
> I am going to construct the template by myself.
> OK. I have fixed bond order and added hydrogens.
> Now I am calling antechamber to assign atom type and partial
> charge.
> Total number of electrons: 302; net charge: 0
> Running: /Users/alan/Programmes/amber11/bin/sqm -O -i -o sqm.out

If the "fastbld" option of sleap doesn't work, then run antechamber by hand:

 antechamber -i dmp.pdb -fi pdb -o dmp.mol2 -fo mol2 -c bcc

followed by

 parmchk -f mol2 -i dmp.mol2 -o dmp.frcmod

Then you can load the dmp.mol2 and dmp.frcmod files into LEaP, and go from

...good luck....dac

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Received on Tue Jun 21 2011 - 06:30:04 PDT
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