On 3/19/20 1:25 PM, Adarsh V. K. wrote:
Dear all, How to overcome this error ? ( ERROR 1 [file lig.itp, line 575]; Duplicate atom index (19) in virtual_sites3) I tried after deleting the line which returned an error message but still the problem does not get resolved. Command line: *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* *The above command returns following 'error message' while using with " ions.mdp "* ---------------------------------------------------------- NOTE 1 [file ions.mdp]: ERROR 1 [file lig.itp, line 575]: Duplicate atom index (19) in virtual_sites3 -----------------------------------------------------------
This comes from our script exploiting a hack allowed in GROMACS 2016 for constructing virtual sites. It is invalid in version 2018 and newer, and you should get the latest version of the script from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs, regenerate the topology, and use GROMACS version 2020, which supports virtual site construction in a manner fully consistent with CHARMM.
-Justin
*I tried after deleting the line 575, but it produces another error at a later stage* gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr gmx mdrun -deffnm nvt -v ------------------------------------------------------------------------------------ starting mdrun 'XX in water' 50000 steps, 100.0 ps. Step 4, time 0.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000442, max 0.021883 (between atoms 5216 and 5218) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 5216 5217 61.7 0.1111 0.1125 0.1111 5216 5218 36.6 0.1111 0.1135 0.1111 Step 5, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 201.336624, max 8789.209961 (between atoms 3384 and 3385) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 3384 3385 128.4 0.1111 976.5923 0.1111 4542 4543 103.1 0.1111 806.7125 0.1111 4542 4544 90.0 0.1111 0.4553 0.1111 5216 5217 90.0 0.1125 0.1590 0.1111 5216 5218 50.4 0.1135 0.1079 0.1111 step 5: One or more water molecules can not be settled. Check for bad contacts and/or reduce the time step if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) ------------------------------------------------------------------------------------------
-- ================================================== 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.