Thanks for the quick reply, I have given this command to add 612 water molecules. genbox -cs spc216 -nmol 612 -cp ala_box.gro -o ala_solv.gro -p ala.top
But in the solvated file, I see there are 668 water molecules. A part of the output while adding water molecules is as follows Using plugin gro for structure file ala_solv.gro Info) Using plugin gro for coordinates from file ala_solv.gro Info) Determining bond structure from distance search ... Info) Finished with coordinate file ala_solv.gro. Info) Analyzing structure ... Info) Atoms: 2026 Info) Bonds: 1357 Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0 Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info) Residues: 671 Info) Waters: 668 Warning) Unusual bond between residues: 1 (none) and 2 (protein) Warning) Unusual bond between residues: 2 (protein) and 3 (none) Info) Segments: 1 Info) Fragments: 669 Protein: 1 Nucleic: 0 On Tue, Aug 14, 2012 at 9:46 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 14/08/2012 2:02 PM, tarak karmakar wrote: >> >> Dear All, >> >> Is there any way to add a specific number of water ( let say 650 >> water) molecules while dissolving the solute in a given box ? > > > Check out genbox -h > > Mark > -- > 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 Tarak -- 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
