[gmx-users] genbox problems
spoel at xray.bmc.uu.se
Sun Aug 18 16:47:01 CEST 2002
On Sun, 2002-08-18 at 14:33, Chris Shaw wrote:
> Hi all,
> Just a quick question. I am getting a feel of gromacs by playing around with helices in different solvents. My problem is that genbox re-writes the .gro file to represent the addition of solvent molecules, but doesn't re-write the .top file to reflect the changes. When I attempt to add the .itp file for example dmso.itp into the top file with the #include command it doesn't seem to register and i get an error back re not being able to define SD atom types. Could any one help, as I am sure that i am doing something fundamentally wrong.
Probably SD is not in the force field you are using for the protein. In
GROMOS96 the atom types may be named differently. Just check all the
topology files, including those from the library (gromacs/share/top).
With the manual in hand it should be straightforward to sort out.
> Many thanks in advance
> Get a bigger mailbox -- choose a size that fits your needs.
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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