[gmx-users] How to solve the "LINCS WARNING" problem (???)
Justin Lemkul
jalemkul at vt.edu
Mon Apr 20 12:41:50 CEST 2020
On 4/20/20 3:51 AM, 변진영 wrote:
> 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??
>
The GROMOS force fields are united-atom. I do not know why ATB offers
all-atom topologies; they are in principle incompatible with the GROMOS
biomolecular force field.
-Justin
>> 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
>>>>> --
>>>>> Gromacs Users mailing list
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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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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
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