[gmx-users] How to solve the "LINCS WARNING" problem (???)
Prasanth G, Research Scholar
prasanthghanta at sssihl.edu.in
Fri Apr 17 13:05:49 CEST 2020
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-request at maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users at 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-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-owner at 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: ??? <byunjy0614 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem
> Message-ID: <E982A1A3-DFCA-4932-8A1A-7D9B3255D34A at 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-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
> >> --
> >> 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-request at 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-request at 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-request at 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-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 17 Apr 2020 10:25:38 +0530
> From: "Prasanth G, Research Scholar" <prasanthghanta at sssihl.edu.in>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] RIN (Residue interaction network) for protein
> ligand interactions
> Message-ID:
> <
> CAGpSbSR1UhXoXuxOeAh7h0F2UKzTgJ_rfXm7zfYKDezxSH3oVQ at 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" <prasanthghanta at sssihl.edu.in>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] atomselection for index group of cyclic rings
> Message-ID:
> <
> CAGpSbSSQBMcpnSvm5nvWq9ZqbiSvUrc1FktAhgwOTyqw6kP60g at 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-sci at outlook.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem
> Message-ID:
> <
> SL2PR04MB30335B7BE660077087DED2CEE0D90 at 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.Schirra at uibk.ac.at>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] atomtype "OE" in charmm36
> Message-ID:
> <412999B95FB6894AAB9B6283E4C20DA126065042 at 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-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 192, Issue 57
> ******************************************************
>
More information about the gromacs.org_gmx-users
mailing list