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
==================================================
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