[gmx-users] Adding_topology_aminoacid

Kukol, Andreas a.kukol at herts.ac.uk
Mon Aug 8 09:45:04 CEST 2011

Dependent on the force field you are using, the topology of free amino acids may not be defined. Look at the content of the rtp-file for your forcefield, if the free amino acid is defined there, you can use pdb2gmx to generate the topology.

Otherwise you have to treat the amino acid as a new molecule and make a topology for it, following the help in HowTo's on the Gromacs website. 
An easy way to make the topology for a free amino acid is to copy the N- and C-terminal definitions from the rtp-file together, change the linkage and dihedrals, assign new (different) charges and then use pdb2gmx.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of shahid nayeem [msnayeem at gmail.com]
Sent: 08 August 2011 06:23
To: Discussion list for GROMACS users
Subject: [gmx-users] Adding_topology_aminoacid

Dear All
I am solvating my protein in a cubical box with a .gro file containing water and one amino acidX. when I run grompp I get error "No such moleculetype aminoacidX" . Should I create de novo .itp file for the amino acidX on proDrg because I tried to include ffbonded.itp and ffnonbonded.itp in .top file but this also gives error in grompp. Creating a new .itp file on ProDrg will again cause problem of charge and parametrization. Since it is individual normal amino acid not present in protein but as insert molecule in solvation box so I think creating new .itp file should not be needed.
shahid Nayeem

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