dear gromacs users, i am new to gromacs (using version 3.3.1) and trying to simulate an enzyme which is covalently bound to a piece of dna i.e. a tyrosine is connected to the dna backbone establishing a phosphodiester group. but each time i try to start the simulation using the G43a1 forcefield there occurs a warning like WARNING 1 [file "blah.itp", line 1020]: No default G96Angle types, using zeroes or WARNING 39 [file "blah.itp", line 1509]: No default Proper Dih. types, using zeroes
i browsed to the mailing list archive and found lots of problems similar to mine but - forgive me - i am not able to fix my problem with these hints. i know that i have to add these angles and dihedrals in the itp or rtp files. But where exactly and how. one example oif a missing angle is the connection from one nucleeotide to the next in the DNA (O3* - P - O1P). Can anyone tell me how to add the missing lines and where to do that exactly (perhaps with a little example) ??? That would be of great help for me. Otherwise I will die unhappy ... Another problem is: where to tell GROMACS that there is a connective bond, angle, dihedral between an aminoacid (the phenolic group of tyrosine) and the DNA backbone ? So if you have any suggestions that could help me, be so kind and try to answer my question. Have a nice day Joe _______________________________________________ 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
