<DIV><SPAN>On 08/03/12, <B class=name>pragna lakshmi </B><pragnapcu@gmail.com> wrote:</SPAN></DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAD6uh5sCq6k1415xgvPOCxXwECEKj+aQYGxe6FFnCbwOG0-NNA@mail.gmail.com type="cite">
<DIV class="mimepart text html">Dear Gromacs Users,<br />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.</DIV></BLOCKQUOTE>
<DIV> </DIV><DIV><A href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</A> has the procedure. You will need to do suitable background reading as suggested there. Please ask a focussed question when you have one :-)</DIV><DIV> </DIV><DIV>Mark </DIV>