Hi Jinyoung Can you please tell which forcefield you are using for these simulations As far as I remember atb server generates gromos compatible parameters, which is a United atom forcefield. Since you said you are interested in an all atom simulation, I'm slightly confused
Regards. On Fri, 17 Apr, 2020, 2:17 PM , < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: How to solve the "LINCS WARNING" problem (???) > 2. RIN (Residue interaction network) for protein ligand > interactions (Prasanth G, Research Scholar) > 3. atomselection for index group of cyclic rings > (Prasanth G, Research Scholar) > 4. Re: How to solve the "LINCS WARNING" problem (Yu Du) > 5. atomtype "OE" in charmm36 (Schirra, Simone) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Apr 2020 13:30:14 +0900 > From: ??? <byunjy0...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > Message-ID: <e982a1a3-dfca-4932-8a1a-7d9b3255d...@gmail.com> > Content-Type: text/plain; charset="us-ascii" > > 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 > -------------- next part -------------- > . > Is the problem from the wrong ligand topology (parameter) file? > > Thank you. > > > 2020. 4. 16. ?? 11:01, Yu Du <ydu-...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of ??? < > 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. ?? 5:08, Yu Du <ydu-...@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-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of ??? < > 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. > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Apr 2020 10:25:38 +0530 > From: "Prasanth G, Research Scholar" <prasanthgha...@sssihl.edu.in> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] RIN (Residue interaction network) for protein > ligand interactions > Message-ID: > < > cagpsbsr1uhxoxuxoeah7h0f2ukztgj_rfxm7zfykdezxsh3...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear All, > > I am interested in viewing the Residue Interaction network during a protein > - ligand simulation. Can someone suggest an easy way to go about it? > > I tried to use gRINN tool but I guess it doesn't work if ligands are > present. > Thanks in advance. > > -- > Regards, > Prasanth. > > > ------------------------------ > > Message: 3 > Date: Fri, 17 Apr 2020 10:27:52 +0530 > From: "Prasanth G, Research Scholar" <prasanthgha...@sssihl.edu.in> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] atomselection for index group of cyclic rings > Message-ID: > < > cagpsbssqbmcpnsvm5nvwq9zqbisvurc1fktahgwotyqw6kp...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > I am interested in measuring the distance between two cyclic rings present > in the residues and ligands over time. Can you kindly suggest how to go > about this? > Specially, if i am interested in measuring the distance between the center > of the two rings over time. Thank you > > -- > Regards, > Prasanth. > > > ------------------------------ > > Message: 4 > Date: Fri, 17 Apr 2020 06:34:48 +0000 > From: Yu Du <ydu-...@outlook.com> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem > Message-ID: > < > sl2pr04mb30335b7be660077087ded2cee0...@sl2pr04mb3033.apcprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jinyoung, > > You made it clear. > > If you do not have special needs in all-atom version of the ligand, you > can also try the united-atom topology of the very same ligand. > > To check the origin of LINCS WARNING, I suggest running MD simulation with > only protein and only ligand in the same process you followed in a divide > and conquer strategy. > > Could you run the following simulation to pinpoint the error? > > (1) Simulation only all-atom ligand in the system. > (2) Simulation only protein in the system. > (3) Simulation only united-atom ligand in the system if it's possible. > > In the end, I noticed that you used ATB topology, so you need to strictly > follow the instruction in the ATB ff file folders for protein-ligand > simulation. > > PS: gmx-users mail list do not receive attachment. > > Cheers, > Yu > > > > ------------------------------ > > Message: 5 > Date: Fri, 17 Apr 2020 08:45:26 +0000 > From: "Schirra, Simone" <simone.schi...@uibk.ac.at> > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] atomtype "OE" in charmm36 > Message-ID: > <412999b95fb6894aab9b6283e4c20da126065...@xmbx3.uibk.ac.at> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Gromacs users, > > I want to simulate polyethylene glycol and I am using a script to build my > .itp and .gro files. The script is designed to work with charmm35r, however > I only found charmm36 available now (I read, that c35r was only temporary). > I thought, it should work with this version as well. > When I try energy minimization, the atomtype OE is not found. OE is used > for the ether oxygen's in the itp file. > I also found an ether toppar file at MacKerell Lab Hompage, however it > seems to be designed for use with charmm rather than gromacs. > Is there a way to convert it for use with gromacs? Or is there another > definition I can use to work with my PEG? Or maybe c35r is still somewhere > around? > > I would be very grateful if someone could help me! > Simone > > > > ------------------------------ > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 192, Issue 57 > ****************************************************** > -- 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.