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

Thu Apr 16 16:01:58 CEST 2020

If you haven't solved your LINCS WARNING, you need to show more details of how you got that problem, including the generation of your ligand topology file. There are maybe some errors in your ligand topology that you didn't figure out.

Cheers,

Yu
________________________________
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: Thursday, April 16, 2020 21:43
To: gmx-users at gromacs.org <gmx-users at gromacs.org>
Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem

Thank you for reply Du, You
You said that "If you want more suggestion, you need to provide some details of the generation of ligand's topology”
Du you mean that I modify my topology file manually??

> 2020. 4. 14. 오후 5:08, Yu Du <ydu-sci at outlook.com> 작성:
>
> 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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