[AMBER] xleap, unit connectivity and atom name

From: Rasha Alqus <rasha.alqus.manchester.ac.uk>
Date: Wed, 17 Jul 2013 08:26:15 +0000

Dear Amber Users,

I have a structure that is formed a units I called GRA, I used antechamber to produce mol2 file and frcmond then I loaded them in xleap and I created this unit, I have checked this unit and every thing is okey , then saved lib,crd,top.pdb. Then I used this unit to produce my structure using combine command then connected the units together using exleap, I saved mol2 file and lib for big structure and I checked its unit and every thing okey. The problem that the connectivity between the unit are sp2 (atom type) ca, and it seem that when I draw these bond and relax my system these bond are not ar, so I edited mol2 file for the big structure replacing the bond type by ar and recreated the unit,lib,ced.top and pdb. The prablom when I load the pdb file in xleap ( in leaprc I loaded gaff force field and lib), xleap shows that the big structure the units are not connected togather, even thougth I have checked its unit and all are connected with the right bond type. can I use the pdb and move to my next step in m
imizing or do I need to edit something.

I visualized the pdb using vmd and all unites are connected.

I have another question about the atom name, can it be problem if atom name start C1......until C1000, or do I need to set the atom name using only characters as in amber manual.


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Received on Wed Jul 17 2013 - 01:30:05 PDT
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