[gmx-users] How to solve the "LINCS WARNING" problem
변진영
byunjy0614 at gmail.com
Fri Apr 17 06:28:38 CEST 2020
Thank you Yu Du
I encountered the problem while I have tried to simulate the protein-ligand complex system.
1. I generated the all atom ligand topology file from the ATB website. And I make both ligand .gro file and protein .gro file by using pdb2gmx and editconf module.
2. Then I run solvation, adding ion, energy minimization step with no problem
3. The problem I mailed is from NVT or NPT equilibration step. During equilibration step, I met the problem mentioned.
I attached my ligand topology file
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.
Is the problem from the wrong ligand topology (parameter) file?
Thank you.
> 2020. 4. 16. ?? 11:01, Yu Du <ydu-sci at outlook.com> ??:
>
> 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 ??? <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. ?? 5:08, Yu Du <ydu-sci at outlook.com> ??:
>>
>> 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 ??? <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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