Make sure your top file #include ff/spc.itp On 2012-06-29 11:35:24AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: > Hi everybody, > I wanted to add water in the box where I put the protein with the command > > genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro > 2>>logErr 1>>logOut > > The result is that I have indeed water (SOL) in the protein file > (3m71_water.gro). But there is a problem in the topology file (3m71.top). > Here I only have the line in the end after [ molecules ] where it is > written how many SOL were added to the structure: > > SOL 14329 > > But in the [ moleculetype ] part of the topology file there is no SOL > mentioned. This causes an error when I want to call grompp. > > SO my question is: why is there no SOL in the [ moleculetype ] part? > > Best, Eva > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
-- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
