[gmx-users] Topology of a neutral single peptide

soumadwip ghosh soumadwipghosh at gmail.com
Mon May 30 16:42:42 CEST 2016

     I am currently working on the interaction of single peptide chains
with some ligands for which I need to keep all the carboxyl functional
groups of a protein protonated, i.e, in the carboxylic acid form and
thereby the peptide should be neutral. I obtained the PDB of Lysozyme at pH
6.8 and tried to make the protein topology. I did the following steps:

1. pdb2gmx -f lysozyme.pdb -o lysozyme.gro -ter -ignh

When prompted I selected CHARMM 27 ff.

Then it asked for the termini as follows:

Linking CYS-6 SG-48 and CYS-127 SG-981...
Linking CYS-30 SG-238 and CYS-115 SG-889...
Linking CYS-64 SG-513 and CYS-80 SG-630...
Linking CYS-76 SG-601 and CYS-94 SG-724...
Select start terminus type for LYS-1
 0: NH3+
 1: NH2
 2: None
 I selected 1. Then

Start terminus LYS-1: NH2
Select end terminus type for LEU-129
 0: COO-
 1: COOH
 2: CT2
 3: CT3
 4: None
I again selected 1 but when the topology was created it showed : Total
charge 9.000 e

Where am I going wrong? Is there a way to obtain a completely neutral
protein chain topology or is it strictly force field specific? Was there
anything wrong with the command line? I am handling protein topology for
the first time, so please excuse me if I am asking for much.

Thanks in advance for your time.

Soumadwip Ghosh
Senior Research Scholar
IIT Bombay

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