Re: [gmx-users] Glycosylation of ASN

[Subhomoi Borkotoky]

Hi,

Have you tried reducing the timestep in mdp?



On Mon, May 4, 2020, 2:52 AM Naba  wrote:

> Dear users and developers,
>
> I have spent extensive amount of time to model glycosylated ASN residues
> covalently linked with N-ACETYL-D-GLUCOSAMINE (NAG) in a glycoprotein using
> Amber99SB-ILDN force field. Though there may be easy way to do this
> with CHARMM-GUI, I want it for Amber force field for maintaining
> consistency of force field usage with respect to the other sets of
> simulations I have performed already.
>
> I have gone through several post on this and planned to give a try. So,
> I've extracted a pair of covalently bound ASN and NAG from the PDB file
> where they present. I have generated the NAG topology parameters using
> GLYCAM_06j-1 force field in Tleap and ACPYPE. I updated aminoacids.rtp,
> ffbonded.itp and all required files as instructed in the manual section 5.6
> and it was successful in equilibrations. After completion of NVT and NPT
> successfully for 500 ps each, around 7 ns of the production MD, I am
> encountered with warnings and ultimately fatal error like following:
>
> Step 3869783, time 7739.57 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.03, max 0.13 (between atoms 23 and 24)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>  21 22   67.60.1090   0.1090  0.1090
>  21 22   67.60.1090   0.1090  0.1090
>  21 22   67.60.1090   0.1090  0.1090
>  21 22   67.60.1090   0.1090  0.1090
>  21 22   67.60.1090   0.1090  0.1090
> ...
> ...
> ...
>
> for many steps
>
> and then
>
> step 3869795: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Segmentation fault  (core dumped)
>
> I checked it repeatedly by minimizing the structure several times using
> other software including a series of vacuum minimization with
> GROMACS-2019.5 using steepest descent and conjugate gradient minimizers.
> But no success.
>
> Please try to give a way to resolve it. If possible.
>
> Regards,
> Naba
>
>
> Nabajyoti Goswami
>
> Research Associate
> Bioinformatics Infrastructure Facility
> Department of Animal Biotechnology
> College of Veterinary Science
> Khanapara,Guwahati 781022
> Assam, India
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Re: [gmx-users] how to generate average structure from trajectory

[Subhomoi Borkotoky]

Hi,
For discarding first 1ns , modify the trajectory with *trjconv* with *-b*
flag. Use the modified trajectory for  cluster analysis with *gmx cluster*
to get an average
structure from a highly populated cluster.


Thanks & Regards,
--
*Subhomoi Borkotoky, Ph. D.*
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.

Alternate E-mail : subho...@yahoo.com

https://scholar.google.co.in/citations?hl=en=1=bJz7GokJ



On Fri, Mar 6, 2020 at 4:31 AM Sadaf Rani  wrote:

> Dear Gromacs users
> I want to get the average structure of a 10ns simulation by discarding
> earlier 1ns run. What is the best way to get the average structure?
>
> Thanks in advance.
>
> Sadaf
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Re: [gmx-users] Listing residues in gromacs

[Subhomoi Borkotoky]

Hi Christian,

Thank you for your reply. The command worked well. I got the indices of the
residues. I want to calculate the occupancies of the residues near my
reference ion within say 0.5 nm. It will help me a lot if you could suggest
something for it. I have tried gmx distance and gmx mindist with the index
file from gmx select, but not successful.

Thanks & Regards,
--
*Subhomoi Borkotoky, Ph. D.*
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.

Alternate E-mail : subho...@yahoo.com





On Tue, Feb 18, 2020 at 6:58 PM Christian Blau  wrote:

> Hi Subhomoi,
>
>
> Yes,
>
> gmx select
>
> can do that (see
> http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html)
> <http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html>
>
>
> For what you want to do, it's beneficial to have a look at the selection
> syntax here
>
> http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html
> <
> http://manual.gromacs.org/documentation/2020/onlinehelp/selections.html?highlight=selection
> >
>
>
> Best,
>
> Christian
>
> On 2020-02-18 13:14, Subhomoi Borkotoky wrote:
> > Hi,
> >
> > Is there any option in gromacs to list residues/atoms around a reference
> > group? I have checked trjorder , but it only gives number of molecules.
> >
> > Thanks & Regards,
> > --
> > *Subhomoi Borkotoky, Ph. D.*
> > Kusuma School of Biological Sciences,
> > Indian Institute of Technology Delhi,
> > New Delhi-110016,
> > India.
> >
> > Alternate E-mail : subho...@yahoo.com
> >
> > https://scholar.google.co.in/citations?hl=en=1=bJz7GokJ
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[gmx-users] Listing residues in gromacs

[Subhomoi Borkotoky]

Hi,

Is there any option in gromacs to list residues/atoms around a reference
group? I have checked trjorder , but it only gives number of molecules.


Thanks & Regards,
--
*Subhomoi Borkotoky, Ph. D.*
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.

Alternate E-mail : subho...@yahoo.com

https://scholar.google.co.in/citations?hl=en=1=bJz7GokJ
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[gmx-users] Listing residues in gromacs

[Subhomoi Borkotoky]

Hi,

Is there any option in gromacs to list residues/atoms around a reference
group? I have checked trjorder , but it only gives number of molecules.

Thanks & Regards,
--
*Subhomoi Borkotoky, Ph. D.*
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.

Alternate E-mail : subho...@yahoo.com

https://scholar.google.co.in/citations?hl=en=1=bJz7GokJ
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Re: [gmx-users] Distance Calculation peptide-membrane

[Subhomoi Borkotoky]

Hi,


Please find the following link.

https://drive.google.com/open?id=0BzFTh9SCRtetd0Eta21XR2hIY0hvZDRqLW9UemRfUl81Q0pz
Thanks & Regards,
--
*Subhomoi B*



On Thu, Dec 26, 2019 at 6:56 PM Justin Lemkul  wrote:

>
>
> On 12/26/19 11:34 AM, Subhomoi Borkotoky wrote:
> > Hi,
> >
> > I am running a peptide-membrane analysis, where I want to check the
> > distance between peptide and membrane over time (between center of mass).
> > However, I am getting a graph like one pasted below even after pbc
> > correction. Kindly suggest a possible solution.
> >
> > [image: image.png]
>
> Image embedding does not work on this mailing list. Please upload an
> image to a file-sharing service and provide a URL.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
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> http://www.thelemkullab.com
>
> ==
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[gmx-users] Distance Calculation peptide-membrane

[Subhomoi Borkotoky]

Hi,

I am running a peptide-membrane analysis, where I want to check the
distance between peptide and membrane over time (between center of mass).
However, I am getting a graph like one pasted below even after pbc
correction. Kindly suggest a possible solution.

[image: image.png]

Thanks & Regards,
--
*Subhomoi B.*
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Re: [gmx-users] how to calculate average structure

[Subhomoi Borkotoky]

Hi

You can check the log file of the cluster output. An average time step will
be given representating the clusters in a tabular format. Note down the
time, accordingly dump it from the trajectory with trjconv. Use an index
file for the protein+ ligand.


Hope it helps.

On Mon, Oct 7, 2019, 11:24 AM mmousivand93  wrote:

> Dear Dr. Subhomoi
>
> Hi,Thanks a lot for your answering. I use the gmx cluster command  as
> follow
>
> "gmx-mpi cluster -f md300.trr -s md300.tpr -n index.ndx -cutoff 0.1 -cl
> cluster.pdb" , then I got a pdb file with different models of my aptamer
> without ligand, I need to check different interaction between aptamer
> and ligand during simulation time.It would be pleasure if you have any
> suggestion.
>
> Thanks a lot
>
> Maryam
>
> On 2019-10-05 08:43, Subhomoi Borkotoky wrote:
>
> > Hi,
> >
> > You can use "gmx cluster" to get an average structure based on RMSD. Just
> > use an appropriate cut-off.
> >
> > Regards,
> >
> > Subhomoi B.
> >
> > On Sat, Oct 5, 2019, 10:01 AM mmousivand93 
> wrote:
> >
> >> Dear all;
> >>
> >> I performed a molecular dynamic simulation(50ns) for a complex
> >> aptamer-ligand and I am going to analysis the interaction between
> >> aptamer and ligand during the simulation,then I will need the average
> >> structure.
> >>
> >> How can I calculate the average structure, is it correct to
> >> use the following command "GMX DCOVAR -F TRAJ.XTC -S TOPOL.TPR -B 801 -E
> >> 1000 -AV .PDB" , when I used the command, I should
> >> select two group as "THE LEAST SQUARES" and "COVARIANCE ANALYSIS", which
> >> group must be selected,aptamer or system or ligand?
> >>
> >> Thanks a lot
> >> --
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Re: [gmx-users] how to calculate average structure

[Subhomoi Borkotoky]

Hi,

You can use "gmx cluster" to get an average structure based on RMSD. Just
use an appropriate cut-off.

Regards,

Subhomoi B.

On Sat, Oct 5, 2019, 10:01 AM mmousivand93  wrote:

> Dear all;
>
> I performed a molecular dynamic simulation(50ns) for a complex
> aptamer-ligand and I am going to analysis the interaction between
> aptamer and ligand during the simulation,then I will need the average
> structure.
>
> How can I calculate the average structure, is it correct to
> use the following command "GMX DCOVAR -F TRAJ.XTC -S TOPOL.TPR -B 801 -E
> 1000 -AV .PDB" , when I used the command, I should
> select two group as "THE LEAST SQUARES" and "COVARIANCE ANALYSIS", which
> group must be selected,aptamer or system or ligand?
>
> Thanks a lot
> --
> Gromacs Users mailing list
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Re: [gmx-users] Using grace in windows

[Subhomoi Borkotoky]

Hi,

You can use qtGrace in Windows directly.

Regards,

Subhomoi B.


On Wed, May 8, 2019, 7:14 PM DEEPANSHU SINGLA 
wrote:

> I am trying to plot graph from gromacs generated xvg files in windows 10
> using Linux subsystem command line. I installed grace using the same
> command line. When I try to plot the graph using grce in the command line
> by using the following command : xmgrace filename.xvg
>
> I get the following error:
>
> Can't open display
> Failed initializing GUI, exiting
>
> Please, guide me help me in ploting the graph in windows.
>
> Sent from Mail for Windows 10
>
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Re: [gmx-users] ramachandran plot

[Subhomoi Borkotoky]

Hi Javed,

I hope *gmx rama* will solve the issue.

http://manual.gromacs.org/archive/5.0.4/programs/gmx-rama.html


Thanks & Regards,
--
*Subhomoi Borkotoky, Ph. D.*
DBT Research Associate,
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.

Alternate E-mail : subho...@yahoo.com





On Wed, Jan 9, 2019 at 3:01 PM  wrote:

> Dear Users
>
> Can anyone suggest me any available tool to analyze ramachandran plot
> timewise for a trajectory?
>
> Thank You
>
> Regards
> Zaved Hazarika
> Research Scholar
> Dept. Of Molecular Biology and Biotechnology,
> Tezpur University,
> India
>
>
>
>
>
>
>
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Re: [gmx-users] Secondary structure propensity.

[Subhomoi Borkotoky]

Thanks for the addition.

On 16 Feb 2018 6:22 pm, "Justin Lemkul" <jalem...@vt.edu> wrote:

>
>
> On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote:
>
>> Hello,
>>
>> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file ,
>> it
>> contains the required information.
>>
>
> Only indirectly, but scount.xvg has all that is needed, the number of
> residues in a given secondary structure as a function of time. From that,
> percentage over time is a trivial scripting task, [(# in SS) / (# of
> residues)]*100.
>
> -Justin
>
> Regards,
>>
>> S. Borkotoky
>>
>> On Fri, Feb 16, 2018 at 1:30 PM, Sundari <sundi6...@gmail.com> wrote:
>>
>> Dear gromacs users,
>>>
>>> can any one please tell me that how we get the secondary structure
>>> propensity or secondary structure content(%) as a function of simulation
>>> time.
>>>
>>> I used "gmx do_dssp" but it gives me number of residues forming the
>>> secondary structure vs simulation time. is it same thing or something
>>> different?
>>>
>>> Thank you in advance..
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] Secondary structure propensity.

[Subhomoi Borkotoky]

Hello,

I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , it
contains the required information.

Regards,

S. Borkotoky

On Fri, Feb 16, 2018 at 1:30 PM, Sundari <sundi6...@gmail.com> wrote:

> Dear gromacs users,
>
> can any one please tell me that how we get the secondary structure
> propensity or secondary structure content(%) as a function of simulation
> time.
>
> I used "gmx do_dssp" but it gives me number of residues forming the
> secondary structure vs simulation time. is it same thing or something
> different?
>
> Thank you in advance..
> --
> Gromacs Users mailing list
>
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-- 
Yours Sincerely,
--
*Dr. Subhomoi Borkotoky, Ph. D.*
DBT Research Associate,
Kusuma School of Biological Sciences,
Indian Institute of Technology Delhi,
New Delhi-110016,
India.


https://scholar.google.co.in/citations?user=bJz7GokJ=en
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Re: [gmx-users] how to generate a trr file

[Subhomoi Borkotoky]

Hi,

You can use "trjconv" command and specify "-e 5".


Hope it helps!!

Regards,

Subhomoi B.

On 17 Sep 2017 8:34 pm, "marzieh dehghan"  wrote:

> Dear all
> Hi
>
> I performed molecular dynamics simulation during 100 ns, but now I want to
> create a trr or xtc file including 50 ns. how I can generate trajectory
> file containing 50 ns from 100 ns of MD run?
>
> thanks a lot
> best wishes
>
> --
>
>
>
>
> *Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
> (IBB)University of Tehran, Tehran- Iran.*
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Re: [gmx-users] Gromacs enquiry

[Subhomoi Borkotoky]

Hi,

You can try the following tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

On Wed, Aug 16, 2017 at 9:48 PM, Odame Agyapong <oagyap...@gmail.com> wrote:

> My name is Odame and I am currently working on a project that requires
> molecular dynamics. I plan using GROMACS for my simulations.
> Specifically I would like to simulate a membrane protein in POPC, TFE,
> DPC and DHPC lipid layers.
>
> First, how do I build or obtain these lipid bilayers. Is there a
> software or online resource I can go to obtain them or gromacs package
> provides these lipids?
>
> Initially i tried a POPC simulation in GROMACS and was getting errors
> in topology outputs. I was therefore unable to continue to the next
> steps .Is there a tutorial specifically for simulating in these
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>



-- 
Yours Sincerely,
--
SUBHOMOI BORKOTOKY,
Centre for Bioinformatics
Pondicherry University
Pondicherry,INDIA.

Alternate Email: subho...@bicpu.edu.in <subho...@mails.bicpu.edu.in>

https://scholar.google.co.in/citations?user=bJz7GokJ=en
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[gmx-users] Regarding sampling convergence

[Subhomoi Borkotoky]

Dear users,

I have a 100 ns simulation trajectory and I have generated FEL (free energy
landscape) with it to extract a minimum energy conformation of my protein.

How can I show sampling convergence of FEL  in gromacs? Do I have to split
the trajectory (say at every 20ns) and generate FELs from them to compare?

-- 
Yours Sincerely,
--
SUBHOMOI BORKOTOKY,
Centre for Bioinformatics
Pondicherry University
Pondicherry,INDIA.

Alternate Email: subho...@mails.bicpu.edu.in

https://scholar.google.co.in/citations?user=bJz7GokJ=en
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[gmx-users] sampling convergence of FEL

[Subhomoi Borkotoky]

Dear users,

I have a 100 ns simulation trajectory and I have generated FEL (free energy
landscape) with it to extract a minimum energy conformation of my protein.

How can I show sampling convergence of FEL  in gromacs? Do I have to split
the trajectory (say 50:50) and generate FELs from both halves to compare?

-- 
Yours Sincerely,
--
SUBHOMOI BORKOTOKY,
Centre for Bioinformatics
Pondicherry University
Pondicherry,INDIA.

Alternate Email: subho...@mails.bicpu.edu.in

https://scholar.google.co.in/citations?user=bJz7GokJ=en
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Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues

[Subhomoi Borkotoky]

Hello,

Please use the "hbond"  utility in gromacs.

gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n
[<.ndx>]][-num [<.xvg>]


On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge <amaligg2...@gmail.com>
wrote:

> Dear Gromacs users,
>
> I carried out 20 ns long MD simulation for my receptor-ligand complex using
> Gromacs software. Now I want to calculate number of hydrogen bonds formed
> in the ligand and receptor corresponding to the residue number. Can anyone
> help me?
>
>
> Thank you.
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-- 
Yours Sincerely,
--
SUBHOMOI BORKOTOKY,
Centre for Bioinformatics
Pondicherry University
Pondicherry,INDIA.

Alternate Email: subho...@mails.bicpu.edu.in
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[gmx-users] Regarding Gromacs compatibilty

[Subhomoi Borkotoky]

Hello,

I would like to know whether it is possible extend a simulation ran with
gromacs 4.6 in gromacs 5. If it is possible, what is the procedure?

-- 
Thanks and Regards,
--
SUBHOMOI BORKOTOKY,
Centre for Bioinformatics
Pondicherry University
Pondicherry,INDIA.

Alternate Email: subho...@mails.bicpu.edu.in
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