[gmx-users] How to solve the "LINCS WARNING" problem (???)
변진영
byunjy0614 at gmail.com
Mon Apr 20 09:50:08 CEST 2020
Hi Prasanth
Firstly Sorry for late reply…
The force field I used is Gromacs 5.x.x 54a7 came from ATB.
I downloaded and used the all-atom topology file(.itp) so I said that it is all-atom simulation.
By any chance, is it wrong approach??
> 2020. 4. 17. 오후 7:58, Prasanth G, Research Scholar <prasanthghanta at sssihl.edu.in> 작성:
>
> 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:
> So
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>> 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
>>>> --
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>> ------------------------------
>>
>> 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
>>
>>
>>
>> ------------------------------
>>
>> --
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>> ******************************************************
>>
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