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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: ??? <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
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------------------------------
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
------------------------------
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