Quoting Thomas Schlesier <[EMAIL PROTECTED]>: > dear all, > till now i simulated with the gromos87 forcefield, but now i want to > change it. > i have two small molecules which consist of a short alkane chain and > then an urea-group. > > i built my molecules with spartan and saved them as .pdb then i tried > pdb2gmx, but this failed: > Fatal error: > Residue 'UNK' not found in residue topology database > but i have no idea how i should name the residues so that they are found > in the database. > then i tried pdb2gmx with my .gro file (which i get from prodrg with the > .pdb file), but here the same problem occured.
Right, because pdb2gmx does not magically produce parameters for any molecule you'd like. Check the .rtp file for the force field you're interested in; it will show you the residues/molecules for which parameters exist. > > the other thing that i tried was to make the files with the beta version > of prodrg. i get the .gro/.g96 and .itp files but they look the same > like the files for the gromos87 forcefield (different values but the > same format). They should look the same; the different parameters are what you're after. Be aware that PRODRG produces charges/charge groups that are often unsatisfactory and need refining. > i used editconf on the .g96 file but it doesn't really work, the new > .g96 file looks like: > > TITLE > > END > POSITION > END > BOX > 10.000000000 10.000000000 10.000000000 > END > > from that and the gromacs-user manual i get the idea that .gro and .96 > files use different formats, but i don't really know how the format for > .g96 looks like (i looked for a user manual for gromos96, but didn't > found one for free). > > so the question is: > 1) is there a way to translate the gromos87 files to gromos96? > or > 2) what should i do with the files form prodrg beta that they work? I'm not quite sure what you're after in these, but I can tell you the following: 1. You don't translate one force field to another, in terms of some simple conversion. You derive new parameters, or use parameters from a well-documented, trusted source. In terms of .g96 --> .gro conversion, editconf should have done the trick. What was the command you tried, and was the .g96 file properly formatted? 2. You use the .itp file you get from PRODRG, verify the validity of the parameters, and proceed. -Justin > > thanks for an answer > thomas > _______________________________________________ > gmx-users mailing list [email protected] > 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
