[gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Hi all,
How can I convert 3 different gromacs itp  file to generate single psf file
?
Is there any command to do that
I tried using top2psf.pl script to do that , but it failed.

Thank you.
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Re: [gmx-users] Distances calculation in umbrella sampling

[Kingsley Theras Primus Dass .]

dear users,
 I am encountering a problem with script, the summary.dat file does
not generate
any value. But if I run the distance command one at the time , it is
generating the value, I could not figure out where I am goingperlgmx wrong.
can anyone tell where lies the mistake?mistake?


Thank you

*below the command line for one distance *
Command line:
  gmx_mpi distance -s sgdp_pull_t.tpr -f conf1.pdb -n index.ndx -oall
dist1.xvgtpr -f conf1.pdb -n index.ndx -oall dist1.xvg -n index. - dist1.xvg
pdbndxoall

Available static index groups:
 Group 0 "System" (89993 atoms)
 Group 1 "Protein" (6541 atoms)
 Group 2 "Protein-H" (5087 atoms)
 Group 3 "C-alpha" (644 atoms)
 Group 4 "Backbone" (1932 atoms)
 Group 5 "MainChain" (2578 atoms)
 Group 6 "MainChain + Cb" (3192 atoms)
 Group 7 "MainChain + H" (3209 atoms)
 Group 8 "SideChain" (3332 atoms)
 Group 9 "SideChain-H" (2509 atoms)
 Group 10 "Prot-Masses" (6541 atoms)
 Group 11 "non-Protein" (83452 atoms)
 Group 12 "Other" (12949 atoms)
 Group 13 "_ *" (19 atoms)
 Group 14 "GDP" (34 atoms)
 Group 15 "POPC" (12896 atoms)
 Group 16 "NA" (107 atoms)
 Group 17 "CL" (106 atoms)
 Group 18 "Water" (70290 atoms)
 Group 19 "SOL" (70290 atoms)
 Group 20 "non-Water" (19703 atoms)
 Group 21 "Ion" (213 atoms)
 Group 22 "_ *" (19 atoms)
 Group 23 "GDP" (34 atoms)
 Group 24 "POPC" (12896 atoms)
 Group 25 "NA" (107 atoms)
 Group 26 "CL" (106 atoms)
 Group 27 "Water_and_ions" (70503 atoms)
 Group 28 "Protein_chain_A" (3536 atoms)
Specify any number of selections for option 'select'
(Position pairs to calculate distances for):
(one per line,  for status / groups, 'help' for help, Ctrl-D to end)

> Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision)
Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision)
Reading frame 0 time 10.000 '', 89993 atoms
Last frame 0 time 10.000
Analyzed 1 frames, last time 0.000
GDP:
  Number of samples: 17
  Average distance: 0.16202 nm
  Standard deviation: 0.05626 nm
Protein_chain_A:
  Number of samples: 1768
  Average distance: 0.19869 nm
  Standard deviation: 0.12505 nm



the error message that I get when I run perl script perl script

readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
readline () on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $ distance in concatenation (.) Or string at
distances.pl line 30.
Cleaning up ...



2017-11-30 23:10 GMT+08:00 Amir Zeb :

> Solved it,
>
> Thanks every one!
>
> Amir
>
> On Thu, Nov 30, 2017 at 5:06 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 11/30/17 4:04 AM, Rose wrote:
> >
> >> Till nowi think the only solution is to use gmx distance for each
> >> conf.gro files.then use perl script.
> >> don't forget to delete gmx distance line from script.
> >>
> >
> > Or run one instance of gmx distance manually to understand how to
> properly
> > use it, diagnose any problems in your selection, etc. and fix the script.
> > There's no reason to reinvent the wheel, just modify the script properly
> to
> > suit your needs.
> >
> > -Justin
> >
> > --
> > ==
> >
> > 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
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? 

Re: [gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Thanks for the answering
I have doubts , because in the gromacs manual , they have mentioned that ,
the application of Essential dynamics is also to enhance the sampling with
respect to usual MD. So, i want to make sure whether my understanding about
ED is correct or not ?


On Oct 19, 2017 5:46 AM, "Dallas Warren" <dallas.war...@monash.edu> wrote:

> Essential Dynamics = extracts the correlated motions of proteins to
> understand the motions that are most fundamental to the activity of
> the protein (http://www.gromacs.org/Documentation/How-tos/
> Essential_Dynamics)
> Accelerated MD = enhanced-sampling method that improves the
> conformational space sampling by reducing energy barriers separating
> different states of a system
> (http://www.ks.uiuc.edu/Research/namd/2.9/ug/node63.html)
>
> Found via a quick search.
>
> From those quick definitions, they do two different things.
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On 17 October 2017 at 21:16, Kingsley Theras Primus Dass .
> <105726...@gms.tcu.edu.tw> wrote:
> > Hi all,
> > I have a very basic question about essential dynamics. I want to know
> > whether essential dynamics function is similar to Accelerated MD ? Or
> > essential dynamics is different from Accelerated MD ?
> >
> > Thanks in advance.
> >
> > Kingsleg Theras
> > --
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> >
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[gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Hi all,
I have a very basic question about essential dynamics. I want to know
whether essential dynamics function is similar to Accelerated MD ? Or
essential dynamics is different from Accelerated MD ?

Thanks in advance.

Kingsleg Theras
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Re: [gmx-users] MM/PBSA

[Kingsley Theras Primus Dass .]

sure 
the below is my command line
qsub /home/hauren32/Desktop/work/MM_PBSA_2.0/GMXPBSAtool/gmxpbsa0-1_TEST.pbs

and the files i have are
1. npt.xtc
2.npt.tpr
2.index.ndx
3.topol.top
4. gdp.itp
5.protein.itp




2017-08-09 12:22 GMT+08:00 Amir Zeb <zebami...@gmail.com>:

> can you please paste your command line here?
> we can judge where you are wrong
>
>
> On Aug 9, 2017 12:50 PM, "Kingsley Theras Primus Dass ." <
> 105726...@gms.tcu.edu.tw> wrote:
>
> Hi everyone,
>
> I am trying to calculate the binding free energy between protein and ligand
> by using MM/PBSA. I included all the .itp files.  But when run the command,
> am getting an error saying "NO XTC" Could someone help me, what would be
> wrong, why such error occurs. i have pasted the error message below.
>
>
> Thank you!
>
>
> Select a group:
> ---
> Program trjconv_mpi, VERSION 4.5.5
> Source code file: trxio.c, line: 832
>
> Fatal error:
> No XTC!
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "You Could Make More Money As a Butcher" (F. Zappa)
>
> Select group for least squares fit
> Selected 27: 'complex'
> Select group for centering
> Selected 27: 'complex'
> Select group for output
> Selected 27: 'complex'
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[gmx-users] MM/PBSA

[Kingsley Theras Primus Dass .]

Hi everyone,

I am trying to calculate the binding free energy between protein and ligand
by using MM/PBSA. I included all the .itp files.  But when run the command,
am getting an error saying "NO XTC" Could someone help me, what would be
wrong, why such error occurs. i have pasted the error message below.


Thank you!


Select a group:
---
Program trjconv_mpi, VERSION 4.5.5
Source code file: trxio.c, line: 832

Fatal error:
No XTC!

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"You Could Make More Money As a Butcher" (F. Zappa)

Select group for least squares fit
Selected 27: 'complex'
Select group for centering
Selected 27: 'complex'
Select group for output
Selected 27: 'complex'
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[gmx-users] Umbrella sampling

[Kingsley Theras Primus Dass .]

Hii
 I am trying out the umbrella sampling tutorial. I finished generating a
series of coordinate file , but when i run the perl script the
summary_distance.dat doesnt generate the COM distance value 
What would be the possible reason for this ?

Thank you
Kingsley
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Re: [gmx-users] B-FACTOR

[Kingsley Theras Primus Dass .]

Thanks for the answer !
I tired that too , but the problem is when we tired viewing the pdb
structure in pymol and MOE software , both show different structural
changes ...

Can you please help me how to over come this problem. How to analyse the
output file of  B-FACTOR  in pymol...?

On 9 May 2017 9:31 p.m., "RAHUL SURESH" <drrahulsur...@gmail.com> wrote:

I am not sure but I think u can calculate t along with rmsf calculation
where you have to generate additional output as pdb file.
On Tue, 9 May 2017 at 6:58 PM, Kingsley Theras Primus Dass . <
105726...@gms.tcu.edu.tw> wrote:

> Hi everyone !
>  I want to calculate b-factor , but I don't kno how to calculate. Can
> anyone please tell me how to calculate b-factor for a protein and how to
> analyse it ...
>
>
> Thanks in advance
> --
> Gromacs Users mailing list
>
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> posting!
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>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] B-FACTOR

[Kingsley Theras Primus Dass .]

Hi everyone !
 I want to calculate b-factor , but I don't kno how to calculate. Can
anyone please tell me how to calculate b-factor for a protein and how to
analyse it ...


Thanks in advance
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[gmx-users] MM/Pbsa

[Kingsley Theras Primus Dass .]

Hi,
 I tried to calculate binding free energy for my protein. I tried using MM
/ PBSA, when i ran the program i am getting an error. Could you please say
why such error is occuring and how should i need to rectify it.



the error message is below


17:54:41
 The directory RUN_ is not present. Please check the INPUT.dat file or run
"gmxpbsa0.pbs".
Exiting -


Thank you.

Kingsley Theras
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[gmx-users] Fwd: error in minimization

[Kingsley Theras Primus Dass .]

-- Forwarded message --
From: Kingsley Theras Primus Dass . <105726...@gms.tcu.edu.tw>
Date: 2017-02-23 18:06 GMT+08:00
Subject: error in minimization
To: gromacs.org_gmx-users@maillist.sys.kth.se, gmx-us...@gromacs.org


Hello !!

I am encountering an error in minimization step. Help me out to avoid this
kind of error.
The error message says,



WARNING: Listed nonbonded interaction between particles 2999 and 3006
At distance 2.442 which is larger than the table limit 2.400 nm.

This is capable capable any
A doubt molecule you are decoupling during a free energy calculation
Since my inward beyond the table can not be computed,
They are skipped until they are inside the table pricing again. You will
Only see this message once, even if it too many rows.

IMPORTANT: This should not happen in a stable simulation, so there is
Something something wrong with your system. Only change the table-extension
Distance in the mdp file if you are really sure that is the reason.

Step 19: Water places starting at atom 63060 can not be settled.
Check for bad contacts and / or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates.


Thank you.
Kingsley
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[gmx-users] error in minimization

[Kingsley Theras Primus Dass .]

Hello !!

I am encountering an error in minimization step. Help me out to avoid this
kind of error.
The error message says,



WARNING: Listed nonbonded interaction between particles 2999 and 3006
At distance 2.442 which is larger than the table limit 2.400 nm.

This is capable capable any
A doubt molecule you are decoupling during a free energy calculation
Since my inward beyond the table can not be computed,
They are skipped until they are inside the table pricing again. You will
Only see this message once, even if it too many rows.

IMPORTANT: This should not happen in a stable simulation, so there is
Something something wrong with your system. Only change the table-extension
Distance in the mdp file if you are really sure that is the reason.

Step 19: Water places starting at atom 63060 can not be settled.
Check for bad contacts and / or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates.


Thank you.
Kingsley
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[gmx-users] error in minimization step

[Kingsley Theras Primus Dass .]

Hello !!

I am encountering an error in minimization step. Help me out to avoid this
kind of error.
The error message says,



WARNING: Listed nonbonded interaction between particles 2999 and 3006
At distance 2.442 which is larger than the table limit 2.400 nm.

This is capable capable any
A doubt molecule you are decoupling during a free energy calculation
Since my inward beyond the table can not be computed,
They are skipped until they are inside the table pricing again. You will
Only see this message once, even if it too many rows.

IMPORTANT: This should not happen in a stable simulation, so there is
Something something wrong with your system. Only change the table-extension
Distance in the mdp file if you are really sure that is the reason.

Step 19: Water matter starting at atom 63060 can not be settled.
Check for bad contacts and / or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
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[gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Dear Users!!


 I have a question about RMSD.  I ran MＤ simulaton for 500ns and connected
all my .xtc files using trjcat command.
And , then I used g_rms command with the connected .xtc file to calculate
RMSD for backbone atoms. But , when I run g_rms command , I get a warning
as follows:



WARNING: If there are molecules in the input trajectory file
 that are broken across periodic boundaries, they
 cannot be made whole (or treated as whole) without
 you providing a run input file.

Can someone say , why this warning msg is coming, and how should i need to
avoid this. what measure should i need to take ?




Thank you.
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Re: [gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Even when I add the new atom types to aminoacid.rtp, .hdb ,   .atp ,
Still it shows the same error 

Could you please suggest some solutions.

Thank you in advance

On 8 Nov 2016 6:59 p.m., "Justin Lemkul" <jalem...@vt.edu> wrote:

>
>
> On 11/7/16 10:44 PM, Kingsley Theras Primus Dass . wrote:
>
>> Hello users!!
>>
>> I generated a Topology file for SO3- using ATB topology generator , which
>> is compatible with GROMACS. Then I copied the .rtp file from ATB and
>> pasted
>> it into  GROMACS aminoacid.rtp.
>>
>>  The  partial charge of aminoacid sulfated-tyrosine was -1.
>> When I run -pdb2gmx there was error saying the atoms were missing ,
>> ---
>> Program gmx pdb2gmx, VERSION 5.1
>> Source code file:
>> /home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreproce
>> ss/pdb2top.cpp,
>> line: 1584
>>
>> Fatal error:
>> There were 6 missing atoms in molecule Protein_chain_D, if you want to use
>> this incomplete topology anyhow, use the option -missing
>>
>>
>> then I ran pdb2gmx -ignh -p topol.top -missing
>>
>> It generated the topology file. But the parital charge of sulfated
>> tyrosine
>> was changed to -2, coz of missing hydrogen atoms.
>>
>> can you please suggest some solutions , to overcome this problem.
>>
>>
> Add an .hdb entry for your residue so that pdb2gmx will build the missing
> atoms.  In general, never use the -missing option.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
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[gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Hello users!!

I generated a Topology file for SO3- using ATB topology generator , which
is compatible with GROMACS. Then I copied the .rtp file from ATB and pasted
it into  GROMACS aminoacid.rtp.

 The  partial charge of aminoacid sulfated-tyrosine was -1.
When I run -pdb2gmx there was error saying the atoms were missing ,
---
Program gmx pdb2gmx, VERSION 5.1
Source code file:
/home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/pdb2top.cpp,
line: 1584

Fatal error:
There were 6 missing atoms in molecule Protein_chain_D, if you want to use
this incomplete topology anyhow, use the option -missing


then I ran pdb2gmx -ignh -p topol.top -missing

It generated the topology file. But the parital charge of sulfated tyrosine
was changed to -2, coz of missing hydrogen atoms.

can you please suggest some solutions , to overcome this problem.




Thank You
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[gmx-users] Fwd: (no subject)

[Kingsley Theras Primus Dass .]

-- Forwarded message --
From: "Kingsley Theras Primus Dass ." <105726...@gms.tcu.edu.tw>
Date: 3 Nov 2016 11:42 a.m.
Subject: [gmx-users] (no subject)
To: <gromacs.org_gmx-users@maillist.sys.kth.se>
Cc:

Hello users !

I want to Add SO3- to tyrosine residue  of my protein. I generated the
topology file for SO3- (TYS) residue using PRODRUG server and incorporated
that topology into my topology. I am using GROMACS45a3 force field . but
still when i try running pdb2gmx , it shows error.

could you please suggest some solution for it .


Program gmx pdb2gmx, VERSION 5.1
Source code file:
/home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/resall.c,
line: 486

Fatal error:
in .rtp file in residue TYS at line:
 1 O 1  TYS   O 1   -0.682  15.9994




Thank you
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[gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Hello users !

I want to Add SO3- to tyrosine residue  of my protein. I generated the
topology file for SO3- (TYS) residue using PRODRUG server and incorporated
that topology into my topology. I am using GROMACS45a3 force field . but
still when i try running pdb2gmx , it shows error.

could you please suggest some solution for it .


Program gmx pdb2gmx, VERSION 5.1
Source code file:
/home/hsulab00/Documents/gromacs-5.1/src/gromacs/gmxpreprocess/resall.c,
line: 486

Fatal error:
in .rtp file in residue TYS at line:
 1 O 1  TYS   O 1   -0.682  15.9994




Thank you
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[gmx-users] (no subject)

[Kingsley Theras Primus Dass .]

Hello !
As I am new to this field , I have some doubts . I want to sulfate the
tyrosine residue in the chemokine receptor ...
But wen I download a pdb file that has sulfated tyrosine residue and run
pdb2gmx command in GROMACS ,it is showing a error message ...how can i come
over this problem

Program pdb2gmx, VERSION 4.6.1

Source code file:
/home/abuild/rpmbuild/BUILD/gromacs-4.6.1/src/kernel/resall.c, line: 642


Fatal error:

Residue 'TYS' not found in residue topology database

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

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[gmx-users] doubts in sulfating in GROMACS

[Kingsley Theras Primus Dass .]

hello !
 I want know to how to sulfate the tyrosine residue in GROMACS? when i try
to sulfate , GROMACS is showing error saying that it is not in the .rtp
file. Kindly, help me with it .



thank you
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