On Thu, Jan 8, 2009 at 2:48 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: >> 2. grompp with the modified topology file returns the following error: >> >> ------------------------------------------------------- >> Program grompp, VERSION 4.0.2 >> Source code file: ../../../SRC/src/kernel/toppush.c, line: 897 >> >> Fatal error: >> Atomtype SD not found >> ------------------------------------------------------- >> >> On searching mailing list archive, I found that there is problem with >> the dmso.itp file: >> http://www.mail-archive.com/gmx-users@gromacs.org/msg15431.html >> >> It seems the "mass" column is missing in dmso.itp even in the latest >> version of Gromacs. Is there any corrected version of this file >> available? Or do I need to manually put these values? It would be nice >> if this file is corrected in some later version. > > I think the problem is mixing of force fields. The dmso.itp included in > /share/top is based on ffgmx. Are you using ffgmx? If so, don't. If you > are using another force field, then you will need to completely update > dmso.itp to correspond to the new parameters. Excellent DMSO parameters > exist under Gromos96 53a6, IIRC. > > The mass column is needed, but is not the cause of your specific problem.
Thanks for your response Justin. I am using the GROMOS96 43a2 force field. I shall try to modify the dmso.itp and dmso.gro accordingly and see what happens. A newbie question: what is the right way to search for existing DMSO parameters under any given force field, e.g. Gromos96 53a6 as you mentioned? Thanks and regards, Suman Chakrabarty. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
