On 10/6/19 4:56 AM, Ayesha Fatima wrote:
Dear All, I m simulating cholesterol membrane with protein embedded in water portion of the upper leaflet of the membrane. I am using Gromacs 2019 built on Windows 10 WSL. My intention is to pull the protein through the membrane from one end to the other into the water part. The membrane was built on CHARMM-GUI and it added the TIP3 water molecules on both sides of the membrane. Using Charmm36 in Gromacs, i prepared the protein without error. I was able to add ions and solvate the system without any issue. Now when I want to minimise it , i am getting warnings when running the grompp to generate the tpr that I would like to understand. I looked on the internet and as per advice looked the TIP3.itp. the warning is: WARNING 1 [file TIP3.itp, line 25]: Too few parameters on line (source file /mnt/e/gromacs/gromacs-2019/src/gromacs/gmxpreprocess/toppush.cpp, line 1326) And line 25 is ;[ settles ] ; i j funct length 1 1 9.572000e-02 1.513900e-01 Also the note below says NOTE 2 [file topol.top, line 1394]: In moleculetype 'TIP3' 3 atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom. I checked line mentioned . given in red [ molecules ] ; Compound #mols Protein_chain_a 1 CHL1 256 TIP3 7171 SOL 67764 CL 1 Any idea how to correct the error? should i have changed the TIP3 to SOL before solvating.
Your topology has [settle] commented out, so the parameters are not correctly interpreted.
Note, however, that you cannot have multiple molecule blocks that use SETTLE, so everything needs to either be TIP3 or SOL; you can't use both simultaneously.
-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.
