[gmx-users] Strange in PMF calculation (Shi Li)
Shi Li
sli259 at g.uky.edu
Wed Nov 23 01:30:05 CET 2016
> 在 2016年11月22日，16:37，gromacs.org_gmx-users-request at maillist.sys.kth.se 写道：
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> Today's Topics:
>
> 1. Re: protein-ligand umbrella sampling (Justin Lemkul)
> 2. Re: Protein-DNA_ligand simulation. (Justin Lemkul)
> 3. Re: question (Justin Lemkul)
> 4. Re: Strange in PMF calculation (Justin Lemkul)
> 5. Re: Protein-DNA_ligand simulation. (Andrea Spitaleri)
> 6. Re: Melting temperature for the lipid bilayer (Mohsen Ramezanpour)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 22 Nov 2016 15:21:16 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] protein-ligand umbrella sampling
> Message-ID: <ddad86bc-c6ea-73a0-4aad-65d867377609 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 11/22/16 6:46 AM, abhisek Mondal wrote:
>> Hi,
>> I'm running the umbrella sampling code for the very first time for
>> protein-ligand system. My goal is to observe how the protein's conformation
>> behaves when I pull the ligand and measure parameters subsequently.
>>
>> The pull code I've been using is:
>> ; Pull code
>> pull = yes
>> pull_ngroups = 2
>> pull_ncoords = 1
>> pull_group1_name = JZ4
>> pull_group2_name = Protein_chain_A
>> pull_coord1_type = umbrella ; harmonic biasing force
>> pull_coord1_geometry = distance ; simple distance increase
>> pull_coord1_groups = 1 2
>> pull_coord1_dim = N N Y
>> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
>> pull_coord1_k = 500 ; kJ mol^-1 nm^-2
>> pull_coord1_start = yes ; define initial COM distance > 0
>>
>> Things are becoming bit hazy while I'm going for indexing. As per tutorial
>> the following guidelines are given:
>>
>> gmx make_ndx -f npt.gro
>> (> indicates the make_ndx prompt)
>>> r 1-27
>>> name 19 Chain_A
>>> r 28-54
>>> name 20 Chain_B
>>> q
>>
>> But can you please help me indexing my system here. I'm not being able to
>> corroborate my system with the given code above.
>>
>> The output of "gmx make_ndx -f npt.gro" is:
>>
>> 1 MET 2 ASN 3 ILE 4 PHE 5 GLU 6 MET 7 LEU 8
>> ARG 9 ILE 10 ASP 11 GLU 12 GLY 13 LEU 14 ARG 15 LEU
>> 16 LYS 17 ILE 18 TYR 19 LYS 20 ASP 21 THR 22 GLU 23
>> GLY 24 TYR 25 TYR 26 THR 27 ILE 28 GLY 29 ILE 30 GLY
>> 31 HIS 32 LEU 33 LEU 34 THR 35 LYS 36 SER 37 PRO 38
>> ASP 39 LEU 40 ASN 41 ALA 42 ALA 43 LYS 44 SER 45 GLU
>> 46 LEU 47 ASP 48 LYS 49 ALA 50 ILE 51 GLY 52 ARG 53
>> ASN 54 CYS 55 ASN 56 GLY 57 VAL 58 ILE 59 THR 60 LYS
>> 61 ASP 62 GLU 63 ALA 64 GLU 65 LYS 66 LEU 67 PHE 68
>> ASN 69 GLN 70 ASP 71 VAL 72 ASP 73 ALA 74 ALA 75 VAL
>> 76 ARG 77 GLY 78 ILE 79 LEU 80 ARG 81 ASN 82 ALA 83
>> LYS 84 LEU 85 LYS 86 PRO 87 VAL 88 TYR 89 ASP 90 SER
>> 91 LEU 92 ASP 93 ALA 94 VAL 95 ARG 96 ARG 97 CYS 98
>> ALA 99 ALA 100 ILE 101 ASN 102 GLN 103 VAL 104 PHE 105 GLN
>> 106 MET 107 GLY 108 GLU 109 THR 110 GLY 111 VAL 112 ALA 113
>> GLY 114 PHE 115 THR 116 ASN 117 SER 118 LEU 119 ARG 120 MET
>> 121 LEU 122 GLN 123 GLN 124 LYS 125 ARG 126 TRP 127 ASP 128
>> GLU 129 ALA 130 ALA 131 VAL 132 ASN 133 LEU 134 ALA 135 LYS
>> 136 SER 137 ARG 138 TRP 139 TYR 140 ASN 141 GLN 142 THR 143
>> PRO 144 ASP 145 ARG 146 ALA 147 LYS 148 ARG 149 VAL 150 ILE
>> 151 THR 152 THR 153 PHE 154 ARG 155 THR 156 GLY 157 THR 158
>> TRP 159 ASP 160 ALA 161 TYR 162 LYS 163 ASN 164 JZ4 165 -
>> 10482 SOL 10483 - 10503 NA 10504 - 10530 CL
>>
>> Little help regarding the would be very nice.
>>
>
> You have to define a sensible reaction coordinate between the protein and ligand
> based on the structural characteristics of the binding site, how occluded it is,
> whether there may be multiple paths, etc. Typically a reference group is a
> residue or set of residue with which the ligand interacts. The path is then set
> by the pulling vector based on the geometry of the system.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 22 Nov 2016 15:24:06 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Protein-DNA_ligand simulation.
> Message-ID: <14419e07-185f-5772-69a6-923ebbfd9b12 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 11/22/16 2:06 PM, maria khan wrote:
>> Dear Gromacs users.
>> Can gromacs is used in Protein -DNA-ligand simulation??f it is used, which
>> forcefield will be used.??
>
> Just about any will work, but CHARMM and AMBER are most commonly used for
> systems like these. You should investigate (in the literature) the suitability
> of current parameter sets in light of how they might affect properties of
> interest (e.g. AMBER99 is a bad choice for DNA because it distorts over time,
> but more recent parmbsc1 is good, similarly CHARMM36 is vastly better than
> CHARMM27 for nucleic acids).
>
>> what will be the method for that type of simulation.kindly answer me in
>> detail.
>
> Simulating a protein-DNA complex is no different from a protein in water.
> You've got a biomolecule in aqueous solvent. The protocol is generally the same.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 22 Nov 2016 15:24:45 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] question
> Message-ID: <7c114e61-75c4-d5a1-2ab0-02285af33b5d at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/22/16 2:01 PM, ?LVARO RODRIGO RUIZ FERN?NDEZ wrote:
>> Dear gromacs users:
>>
>> I need to build a phospholipid bilayer, but for some reason it gets water, I
>> think the problem could be solved with the construction of a plane that
>> prevents the passage of water molecules. In short, can GROMACS generate a
>> plane that prevents the passage of one type of molecules?.
>>
>
> Yes, this can be done with a flat-bottom restraint. See the manual for
> available options.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 22 Nov 2016 15:25:17 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Strange in PMF calculation
> Message-ID: <86d37293-3186-389a-7575-8922a9196451 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 11/22/16 3:14 PM, Li, Shi wrote:
>> Dear Gromacs users,
>>
>> I am doing some PMF simulations of 2 molecules in vacuum and my resulting
>> profile has a strange look. I attached an eps files here, anyone can give
>> me some suggestion on why there is fluctuation at longer distance?
>>
>
> The mailing list does not accept attachments. Upload an image to a file-sharing
> service and provide the URL.
>
> -Justin
>
Thank you Justin,
Here is the link to my eps file.
https://www.dropbox.com/s/bc2ch1nujm0f825/syn.eps?dl=0 <https://www.dropbox.com/s/bc2ch1nujm0f825/syn.eps?dl=0>
Shi
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 22 Nov 2016 21:33:30 +0100
> From: Andrea Spitaleri <andrea.spitaleri at iit.it>
> To: <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Protein-DNA_ligand simulation.
> Message-ID: <3583cbab-2734-13a8-2798-5708722ec505 at iit.it>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> You can think to use AMBER14SB too which contains the stable bsc0
> parameters:
>
> "Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA"
>
> or as Justin suggested the new bsc1 from Orozco
>
> http://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html
>
> http://mmb.irbbarcelona.org/BigNASim/help.php?id=download
>
> HTH
>
> and
>
>
> On 22/11/2016 21:24, Justin Lemkul wrote:
>>
>>
>> On 11/22/16 2:06 PM, maria khan wrote:
>>> Dear Gromacs users.
>>> Can gromacs is used in Protein -DNA-ligand simulation??f it is used,
>>> which
>>> forcefield will be used.??
>>
>> Just about any will work, but CHARMM and AMBER are most commonly used
>> for systems like these. You should investigate (in the literature)
>> the suitability of current parameter sets in light of how they might
>> affect properties of interest (e.g. AMBER99 is a bad choice for DNA
>> because it distorts over time, but more recent parmbsc1 is good,
>> similarly CHARMM36 is vastly better than CHARMM27 for nucleic acids).
>>
>>> what will be the method for that type of simulation.kindly answer me in
>>> detail.
>>
>> Simulating a protein-DNA complex is no different from a protein in
>> water. You've got a biomolecule in aqueous solvent. The protocol is
>> generally the same.
>>
>> -Justin
>>
>
> --
> Andrea Spitaleri PhD
> Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
> ISTITUTO ITALIANO DI TECNOLOGIA
> Via Morego 30, 16163 - Genova, Italy
> https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
> cell: +39 3485188790
> https://iit.it/people/andrea-spitaleri
> ORCID: http://orcid.org/0000-0003-3012-3557
>
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 22 Nov 2016 14:37:21 -0700
> From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Melting temperature for the lipid bilayer
> Message-ID:
> <CAERzrhu9KtrYt0FpjRMGs9LVMhyuAza5c8ucJz4pneYqLd+BhQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Justin,
>
> Comments interspersed.
>
> On Tue, Nov 22, 2016 at 1:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/21/16 3:28 PM, Mohsen Ramezanpour wrote:
>>
>>> Dear gromacs users,
>>>
>>> Running simulation on a lipid bilayer made by Charmm-GUI, there is about
>>> 24
>>> degrees difference between the reported temperature in Avanti and what I
>>> see in my simulations for getting a liquid disordered (L_disorder)
>>> bilayer.
>>>
>>>
>> How are you quantifying the transition in the simulation?
>
> Mainly by diffusion constant and diffusion graph. However, diffusion
> constant, bilayer thickness and area per lipid all have a shift.
> Order parameters are also higher for lower temperatures.
>
>>
>>
>> I am using all-atom Charmm36 FF for simulations.
>>>
>>
>> What is the lipid?
>>
> DSPS
>
>>
>> I know that it is not possible to get an exact match between experimental
>>> and simulation T values for L_alpha phase of bilayers, but I am not sure
>>> if
>>> these gap seems reasonable or there is something wrong in my simulations.
>>> I
>>> have checked the bonds in tails and apparently, everything looks fine with
>>> topology.
>>>
>>>
>> A gap of 24 degrees is quite substantial. I would not consider that
>> outcome to be sufficiently accurate.
>>
>
> The melting temperature for DSPS is 68 centigrade (341 K). The
> liquid_disordered one is about 365 K (at least one with reasonable
> characteristics of liquid_disorder phase).
>
>>
>> However, based on this, doing simulation in L_alpha phase requires hight T
>>> values (close to 85 or 90 degrees of centigrade) which makes me worry
>>> about
>>> the water molecules in the system. It is a high temperature for water
>>> molecules.
>>>
>>>
>> Agreed, but TIP3P has a ton of other problems, so this is probably the
>> least of our concerns at the moment.
>>
>
>> -Justin
>>
>> Its worth mentioning that bilayer structural properties like lipid order
>>> parameters match available experimental data for these high T values.
>>>
>>> Please let me know your opinion.
>>>
>>> Cheers
>>> Mohsen
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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