[gmx-users] How to solve the "LINCS WARNING" problem

[Yu Du]

Hi Jinyoung,

I guess that the LINCS WARNING you encountered maybe came from hiden errors in the configuration of either protein or ligand OR more directly from the ligand's topology. You need to carefully check the configuration of protein and ligand, e.g. side chain goes through benzene ring.

After a careful check, If you want more suggestion, you need to provide some details of the generation of ligand's topology.

Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275
________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of 변진영 <byunjy0614 at gmail.com>
Sent: Tuesday, April 14, 2020 14:32
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: [gmx-users] How to solve the "LINCS WARNING" problem

Dear GROMACS users,

Since I have run the nvt  and npt processes for the protein-ligand interaction, I met the the warning messages below

Step 231785, time 463.57 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000176, max 0.003912 (between atoms 3035 and 3037)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   3035   3036   34.0    0.1090   0.1087      0.1090

….

Step 231825, time 463.65 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   3024   3025   90.0    0.1090   0.1236      0.1090
   3026   3027  100.8    0.1090   6.6242      0.1090
   3028   3029  162.5    1.7683 5245.4102      0.1090
   3033   3034  106.7    0.1090 426.5654      0.1090
   3035   3037   90.0    0.3851   0.7991      0.1090
   3038   3039   90.0    0.6045   0.4497      0.1090
   3038   3040   90.0    0.1123   0.2833      0.1090
   3041   3042   59.0    0.1020   0.1020      0.1020
Wrote pdb files with previous and current coordinates

Step 231826, time 463.652 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
   1423   1424  140.4    0.1000 503.9983      0.1000
   3024   3025   61.1    0.1236 223337872.0000      0.1090
   3026   3027  168.8    6.6242 149263.5000      0.1090
   3028   3029  165.8  5245.4102 263929.4375      0.1090
   3031   3032  116.2    0.1090 223428336.0000      0.1090
   3033   3034  179.9  426.5654 446766720.0000      0.1090
   3035   3036   35.3   29.6105 831.0708      0.1090
   3035   3037  102.9    0.7991 775.3371      0.1090
   3038   3039   90.0    0.4497   0.6355      0.1090
   3038   3040   47.7    0.2833   0.1111      0.1090
step 231826: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

So I checked the my input configuration. the 3035, 3028, 3035 atoms are ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms.
Why does the LINCS warning      occurs? and How I solve this problem?

Many Thanks

Jinyoung
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