On 9/22/18 2:31 AM, Alex wrote:
Actually, I'd like to know, too. I keep seeing this warning for systems that are fully described in their topologies and all parameters appropriately present in ffnonbonded, etc, i.e. everything passes grompp and runs perfectly fine. I never really paid much attention to this warning, thinking that gmx solvate has its own way of looking things up elsewhere, but an explanation would be nice. I searched the list, but only found reference to the -shell option, which I am not using. What's happening?
This generic warning shows up for any program that uses atomic radii but has not been provided a .tpr file, which contains unambiguous masses and atom types. The warning just alerts the user to the possibility that something strange might happen when guessing what an atom is based solely on its name. For example, "CA" is often the alpha-carbon in proteins, but could it be a calcium ion in some cases? Similarly, is "HG" a hydrogen at the gamma-position or is it mercury?
-Justin
Thanks, Alex On Sat, Sep 22, 2018 at 12:14 AM AKANXA TIWARI <akanxatiwar...@gmail.com> wrote:hello i am simulating tubulin heterodimer . after giving command for solvent adding i got a warning on screen what should i do. Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmx solvate uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 7x7x7 boxes Solvent box contains 202791 atoms in 67597 residues Removed 17799 solvent atoms due to solvent-solvent overlap Removed 10800 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 58064 residues Generated solvent containing 174192 atoms in 58064 residues Writing generated configuration to 1jff_solv.gro Output configuration contains 182636 atoms in 58902 residues Volume : 1882.42 (nm^3) Density : 1006.94 (g/l) Number of solvent molecules: 58064 Processing topology Adding line for 58064 solvent molecules with resname (SOL) to topology file (topol.top) Back Off! I just backed up topol.top to ./#topol.top.1# GROMACS reminds you: "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart) -- 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.
-- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 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.
