Hi,
For 1, I can't say, unless I see the input, but it could be that the Link atoms was not included in the QM groups? For 2, make sure the virtual_sites2 entry is complete, i.e.: Linkatom QMatom MM atoms 1 d(QMatom-Linkatom)/d(QMatom-MMatom) The latter is thus the fraction between the two bondlengths, for hydrogen link atoms something between .6 and .7 or so. Gerrit Deal All, Does anybody have experience doing QMMM simulations. I am interfacing Gromacs 4.5.7 with Gaussian 09-C.01 via Gerrit Groenhof's gau script. I have 2 questions: 1. I was performing a toy run for QMMM ONIOM using lysozyme. I was treating the side chain of one of the lys residues as the QM layer. I was able to successfully generate the .tpr via grompp, and start the md run. The problem is that the Gaussian input files (input.com as produced by gau) seem to be missing the link atom that connects the lys residue to the rest of the protein. I have followed the procedure as listed here exactly for setting up my simulation: http://wwwuser.gwdg.de/~ggroenh/SaoCarlos2008/html/qmmm.html#ndx. Do you know what could be wrong? Is it an error in the gau script? 2. Next, I went ahead and tried to perform a similar run to the one described above with my real system, which is large and has 144 QM atoms and 7 link atoms. This time, I did not even get past the grompp stage. The error I get from grompp is: ------------------------------------------------------- Program grompp, VERSION 4.5.7 Source code file: vsite_parm.c, line: 797 Fatal error: Automatic parameter generation not supported for Virtual site 2 atom 2458 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Does anybody know what could be causing this fatal error? Atom 2458 is the first link atom, as listed in my .gro coordinate file. I looked online, and, regarding a similar error (except pertaining to "Virtual site 3"), it was suggested that constraints be set to all-bonds in the .mdp. My constraints is definitely set to all-bonds. Thank you in advance! Zach Smithline -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.