[gmx-users] Residue 'NAG' not found in residue topology database

Mark Abraham mark.abraham at anu.edu.au
Thu Mar 8 10:19:43 CET 2012

On 08/03/12, pragna lakshmi <pragnapcu at gmail.com> wrote:

> Dear Gromacs Users,
> My Protein has three N-acetyl glucosamine (NAG) residues, UDP and Mn. I have to simulate this protein. I am using a gromacs version of 4.5.3. When i did pdb2gmx step, i understood that NAG is not present in the residue topology database. I used GROMOS96 53a6 force field as i am going to use topology of UDP from prodrg server. I understood that i have to add parameters regarding NAG in aminoacids.rtp, aminoacids.hdb, ffbonded.itp, gbsa.itp and residuetypes.dat. But i am not able to understand what should i mention. Could any body of you please help me out in solving this problem. Thanks in advance.

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field has the procedure. You will need to do suitable background reading as suggested there. Please ask a focussed question when you have one :-)
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