[gmx-users] protein-ligand umbrella sampling
abhisek Mondal
abhisek.mndl at gmail.com
Wed Nov 23 08:07:41 CET 2016
With the above mentioned settings, I tried to run:
*gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
-o pull.tpr*
Got a lot of NOTE as:
NOTE 1 [file md_pull.mdp, line 65]:
md_pull.mdp did not specify a value for the .mdp option "cutoff-scheme".
Probably it was first intended for use with GROMACS before 4.6. In 4.6,
the Verlet scheme was introduced, but the group scheme was still the
default. The default is now the Verlet scheme, so you will observe
different behaviour.
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'optimize_fft'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
NOTE 2 [file md_pull.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
NOTE 3 [file md_pull.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 4 [file md_pull.mdp]:
leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
Feels like a huge version clash is happening. Can I get some views on these
comments. NOTE 3 seems to come more often in my cases.
I'm attaching the md_pull.mdp here.
Thanks
On Wed, Nov 23, 2016 at 11:58 AM, abhisek Mondal <abhisek.mndl at gmail.com>
wrote:
> 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
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>
>
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>
--
Abhisek Mondal
*Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*
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