I am using gromacs for the first time . I have installed gromacs 5.0.4
version and i want to check a miscelle is formed or not using 5 different
ligands in different ratios. I have gone through all basic tutorials on
how to use gromacs ( lysosyme,protein-ligand).
But i am stuck with the problem o
topology with oplsa.ff and include drug.itp files in
that topology file.
On Sunday, September 13, 2015, Justin Lemkul wrote:
>
>
> On 9/11/15 11:59 PM, Chetan Puri wrote:
>>
>> I am using gromacs for the first time . I have installed gromacs 5.0.4
>> version and i want to
presentation .
so can you please help me out with this thing and also is there any other
way by using gromacs and packing a system of different ligands (gromacs
version 5.0.4)
On Sun, Sep 13, 2015 at 6:43 PM, Justin Lemkul wrote:
>
>
> On 9/13/15 3:47 AM, Chetan Puri wrote:
>
>&
torial just to make .tpr file.
i hope this is of not great concern and i would also like to know that why
was grompp not able to read itp files even though i have placed the same
name in every file.
On Mon, Sep 14, 2015 at 10:13 PM, Justin Lemkul wrote:
>
>
> On 9/14/15 11:18 AM, Ch
so what is the best option for topologies.
On Wed, Sep 16, 2015 at 2:19 AM, Justin Lemkul wrote:
>
>
> On 9/15/15 11:35 AM, Chetan Puri wrote:
>
>> thanks for you help and today i was able to solve the problem,
>> actually my pdb file was made using packmole for 5
various molecules and use
it .
On Wed, Sep 16, 2015 at 5:20 PM, Justin Lemkul wrote:
>
>
> On 9/15/15 11:01 PM, Chetan Puri wrote:
>
>> so what is the best option for topologies.
>>
>>
> A force field you trust in concert with molecules that are individually
> par
Is there any way to use maestro cms file for md simulations in gromacs.
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Can somebody suggest what could be the best possible way for generating
small molecules topology file and charge determination ( OPLS force field)
as I want carry out a simulation for miscell formation between small
ligands.
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Can somebody suggest what could be the best possible way for generating
small molecules topology file and charge determination ( OPLS force field)
as I want carry out a simulation for miscell formation between small
ligands.
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I am trying to do a protein- ligand simulation.
And the prodrg server provides the ligand out put by completely removing
the double bonds(making it saturated)
So is there any way to do it.
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it the way aromatic ring is supposed to be after passing through
prodrg.
On 5 Jul 2016 10:26 pm, "Justin Lemkul" wrote:
>
>
> On 7/5/16 10:50 AM, Chetan Puri wrote:
>
>> I am trying to do a protein- ligand simulation.
>>
>> And the prodrg server provides the li
I want to do a protein ligand MD in GROMACS using OPLS-AA force field,
So can someone suggest how to proceed with ligand topology file.
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I want to do a protein ligand MD in GROMACS using OPLS-AA force field,
So can someone suggest how to proceed with ligand topology file.
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I am from Organic chemistry background and I don't know much about
inorganic chemistry calculations.
So I would request you if you could guide me , how to generate a topology
file for a small molecule. e.g. ATP or benzoic acid for OPLS ff
On 21 Feb 2017 11:34 pm, "Justin Lemkul" wrote:
On 2/2
I have few questions
1) I tried topolgen script but it doesn't assign proper atoms, so if I
change the atom type, what will happen to bonds and angles
2) can we use Desmond output for gromacs directly
On 22 Feb 2017 7:29 am, "Chetan Puri" wrote:
> I am from Organic chemistr
I want to use Desmond out.cms file for gromacs, as I want to compare MD
output from Desmond and gromacs .
Since Desmond uses OPLS, I will also be needing OPLS in Gromacs
On 24 Feb 2017 12:11 am, "Justin Lemkul" wrote:
>
>
> On 2/23/17 10:53 AM, Chetan Puri wrote:
>
>&g
I want to determine permeability of drug molecules through various lipid
membranes.
Building the membrane i am able to do with the kalp-dppc tutorial, but for
placing the drug molecule above the membrane i am not getting proper
solution.
So can someone suggest how to place the drug molecule above
I have tried to do an umbrella sampling for a ligand (drug) and membrane as
per the gromacs tutorial. Now i want to calculate permeability and
diffusibility for this ligand, so can anyone suggest how to proceed further.
Since there is some literature available but it does not show the proper
method
Thanks for the reply,
But I could not understand what you want to say,
Since I am trying to do the ligand and membrane simulation while
constraining
the lipid
CHETAN
On 6 Nov 2017 5:24 pm, "Justin Lemkul" wrote:
>
>
> On 11/6/17 12:22 AM, Du, Yu wrote:
>
>> Hi, Justin,
>>
>> Thanks for your ques
I am trying to do umbrella sampling for a ligand and dopc membrane.
For umbrella sampling pulling step, I am unable to posre_restrain the
lipid, since grompp gives a error due to conflict between posre_restrain
file of lipid and itp file of lipid.
I have 128dopc molecules.
So can someone suggest h
n the lipids, you perturb their dynamics and likely influence
the free energy of permeation across the membrane "
So can you please explain in more simple way .
CHETAN
On 11/14/17 9:32 AM, Chetan Puri wrote:
> I am trying to do umbrella sampling for a ligand and dopc membrane.
> For
Can someone guide me in how to make a group for atoms number 1566, 1567,
1569,1571,1574&1579, which all belong to a tyrosine residue number 128 of
protein.
Since I need to measure distance between two groups (ligand and protein)
Regards,
Chetan
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Yes, I have tried but I am having trouble in making a group for atoms with
different numbers.
On Wed, 11 Jul 2018, 22:29 Quyen V. Vu, wrote:
> Have you try make_ndx tool of Gromacs?
>
> On Wed, Jul 11, 2018, 00:09 Chetan Puri wrote:
>
> > Can someone guide me in how to make
you can just manually make the index file as Sohaib
> suggested. An index group is just:
>
> [ name_of_group ]
> ;atomnr of atoms that make up the group eg.
> 1566 1567 1569 1571 1574 1579 etc..
>
> On 12 July 2018 at 16:24, Chetan Puri wrote:
>
> > Yes, I have t
I want to determine if new pockets are developed during md simulation of a
protein using fpocket.
So is there any way we can convert the trajectory file to individual pdb
files or is there any way we can do it in Gromacs
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Thanks for the reply
On 26 Apr 2017 8:53 pm, "Justin Lemkul" wrote:
>
>
> On 4/26/17 11:21 AM, Chetan Puri wrote:
>
>> I want to determine if new pockets are developed during md simulation of a
>> protein using fpocket.
>> So is there any way we can conve
Is there any example or tutorial for building a polymer topology/itp file.
I need for PVP.
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I am trying to install Gromacs 5.1.4 on centos7 with gpu Tesla k40
But on the make step I am getting error
nvcc fatal : unsupported gpu architecture 'compute_20'
So can anyone suggest how to resolve it.
CHETAN
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t; e.g. 2016.4.
>
> Mark
>
> On Tue, Oct 17, 2017 at 11:34 AM Chetan Puri
> wrote:
>
> > I am trying to install Gromacs 5.1.4 on centos7 with gpu Tesla k40
> > But on the make step I am getting error
> > nvcc fatal : unsupported gpu architecture 'compute_20
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