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
. Is the problem from the wrong ligand topology (parameter) file? Thank you. > 2020. 4. 16. 오후 11:01, Yu Du <ydu-...@outlook.com> 작성: > > 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-boun...@maillist.sys.kth.se > <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of 변진영 > <byunjy0...@gmail.com> > Sent: Thursday, April 16, 2020 21:43 > To: gmx-us...@gromacs.org <gmx-us...@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-...@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-boun...@maillist.sys.kth.se >> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of 변진영 >> <byunjy0...@gmail.com> >> Sent: Tuesday, April 14, 2020 14:32 >> To: gmx-us...@gromacs.org <gmx-us...@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 >> -- >> 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. >> -- >> 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. > > -- > 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. > -- > 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.
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