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 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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 gmx-users-requ...@gromacs.org.