[gmx-users] protein-ligand umbrella sampling
abhisek Mondal
abhisek.mndl at gmail.com
Wed Nov 23 07:28:52 CET 2016
Hi,
I have came across that there are many ways of pulling, although have no
idea which is to apply and when. A descriptive tutorial is what I'm missing.
However, I'm thinking to go for distance pulling in all dimension as also
suggested here
<http://thread.gmane.org/gmane.science.biology.gromacs.user/52710>. Please
give me a sanity check. The scenario is my ligand is buried in a
hydrophobic cleft of the protein.
Thank you
On Wed, Nov 23, 2016 at 1:51 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ==================================================
>
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--
Abhisek Mondal
*Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*
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