Hi All. I wish to analyse the dynamics of t4 Lysozyme with a small peptide attached via a disulphide bond.
My MD runs are fine, however I wish to add the ligand N-acetyl glucosamine (NAG) in the active site to measure some distances from the attached peptide to the NAG molecule. I have initially followed John Kerrigan's Drug-Enzyme complex tutorial. ie. Use ProdRG3 sever to generate a gromos87 .itp for NAG, edit the target.gro, to append the NAG atoms, edit target.top and add: #include "nag.itp" and [ molecules ] NAG 1 My problem comes about, I wish to use the GROMOS96 forcefield (from what I have read only the GMX force field works) and when I run grompp I get complaints about a missing atom "CS2". >From searching this archive I see: * I need to modify nag.itp to be GROMOS96 compatible. (NOTE: when comparing an example GROMOS96 .itp to the GROMOS87 .itp there does not seem to be any significant differences besides formatting). Can someone point me in a direction of how to go about this? Can I edit ffG43a1.atp and add these missing atoms? Furthermore, has anybody successfully done something similar to this - performing a simulation with t4Lys:NAG? Any help would be appreciated Cheers Mitch _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
