[gmx-users] Incorrect C-terminal in peptide starting with GLY

Krzysztof Kuczera kkuczera at ku.edu
Tue Aug 24 16:21:44 CEST 2010

Hi gmx-users
I am trying to set up a simulation of a 16-residue peptide that starts 
with GLY and ends with GLU
(PDB attached) using OPLS-AA/L and gromacs-4.5-beta3. Here is the 
pdb2gmx command

pdb2gmx -inter -ignh -f b-hp41-56.pdb -p peptide.top -o peptide.gro

the ff, water, ionization state selection goes well,
 I get a selection of N-terminals that includes GLY-NH3+ which is fine
but then the selection of C-terminals does not have COO-, but only GLY-COO-
- as a result the C-terminal GLU ends up with incorrect charge and qtot 
is not an integer

Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ...

Could someone suggest a fix for this ?


Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkuczera at ku.edu

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