[gmx-users] N-terminus charge

Germana Paterlini germana at certusoft.com
Fri Jan 24 17:09:57 CET 2003

I am new to the list.
The following questions may be an old one... but it is painfull to search in the archive when e-mails don't have subjects...

I am using pdb2gmx with the "-ter" option to choose the charge of the N- and C-termina.

My original pdb file contains a NH3+ and a COO-.

pdb2gmx correctly converts the COO- to COOH. However, the NH3+ did not changed to NH2.
As a way around, I eliminated the hydrogens of NH3+ from the PDB file and then pdb2gmx gave me an NH2
group. However, the nitrogen type is listed as "NL". Shouldn't this be an "NT" ? 
Is this a bug in the TBD file (I used ffG3b1-n)?


Germana Paterlini, Ph.D.
Certusoft, Inc.
7831 Glenroy Road
Suite 440
Minneapolis, MN 55439
germana at certusoft.com

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