Hi, The hard-coded SOL reference that Justin mentioned has been fixed in Gromacs 2018.3 and 2019. If you upgrade your gromacs version, gmx solvate should work as intended.
Kevin > On Jan 20, 2019, at 3:11 PM, Justin Lemkul <[email protected]> wrote: > > > >> On 1/20/19 3:04 PM, ZHANG Cheng wrote: >> In the command >> >> >> gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768 >> -radius 0.21 -p dppc.top >> >> >> 768 waters are added, resulting in the "waterbox.gro". >> >> >> However, the "dppc.top" is not updated for its "[ molecules ]" section. I >> can of course manually add that. But why it is not automatically done? >> >> >> The prompt also shows "0" for "Number of SOL molecules": >> >> >> Generating solvent configuration >> Will generate new solvent configuration of 3x3x3 boxes >> Solvent box contains 4435 atoms in 4435 residues >> Removed 1235 solvent atoms due to solvent-solvent overlap >> Removed 1286 solvent atoms due to solute-solvent overlap >> Sorting configuration >> Found 1 molecule type: >> W ( 1 atoms): 768 residues >> Generated solvent containing 768 atoms in 768 residues >> Writing generated configuration to waterbox.gro >> >> >> Output configuration contains 2304 atoms in 896 residues >> Volume : 421.875 (nm^3) >> Density : 639.416 (g/l) >> Number of SOL molecules: 0 > > solvate is hard-coded to only recognize "SOL" explicitly. You added something > called "W," so solvate doesn't know what that is. Update your topology > manually if you're doing something non-standard (coarse-grain systems qualify > as such). > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > [email protected] | (540) 231-3129 > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thelemkullab.com&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C21926fb8415d4145ccdb08d67f13715e%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636836118819695047&sdata=S2dfOkavrzMqKQqRBapZpTwzTGPIh%2Byt4h9BwKFGr%2Bk%3D&reserved=0 > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C21926fb8415d4145ccdb08d67f13715e%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636836118819695047&sdata=cPfsVvs8Noh1IvrSEHcwkrn7SK2jk0FgXdHodtAc%2BSg%3D&reserved=0 > before posting! > > * Can't post? Read > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C21926fb8415d4145ccdb08d67f13715e%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636836118819695047&sdata=qXurm4P0K1Pd5006fm8FaLCp2zL1fy4adUHW9zitTJQ%3D&reserved=0 > > * For (un)subscribe requests visit > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C21926fb8415d4145ccdb08d67f13715e%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636836118819695047&sdata=SPxNZ2lU24Nw%2BDCIuu8vGcTTzxl53dwsTA4pd2L%2Fb9k%3D&reserved=0 > or send a mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
