[gmx-users] Re: error with g_dist

[chinnu657]

I won't be submitting these though. just letting you know. I just need to
explain how all of these can be achieved. Just clarifying.

But thank you for all the help you've provided. It's been very valuable
help.

Chinnu



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[gmx-users] Re: error with g_dist

[chinnu657]

ok that's ok then. this was the school system. so I can't really reinstall
it. I'll try and use a cluster. Hopefully, it works.

thanks a lot

Chinnu



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Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 6:03 PM, chinnu657 wrote:

Mine still gives me the same error. I don't quite understand why since it's
giving u the right output. Im using the same version as you too.



My guess would be that your installation is buggy, usually the fault of a 
bad/outdated compiler.  Without significantly more detail about how your 
software was compiled and installed, it's simply conjecture, but a probable 
cause.  You could also try installing version 4.6.3, but I doubt the problem 
lies in Gromacs and rather the compilers, libraries, etc. available on your system.



If you do not mind, could you give me the .xvg file? So that I can use it as
a result. Simultaneously, I'll see what I can do to solve the problem with
your help?



I would be far more concerned with the fact that your Gromacs installation 
produces spurious error messages - who knows what else might be wrong?  Me 
providing you with a single number, which is not necessarily representative of 
any ensemble, does you no good.  I'm also not comfortable with providing someone 
with a data file so they can use it for a "submission" (as you called it 
earlier), which seems to imply some sort of assignment, given that it appears 
you are working through one of my tutorials.


-Justin

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==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
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jalem...@outerbanks.umaryland.edu | (410) 706-7441

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[gmx-users] Re: error with g_dist

[chinnu657]

Mine still gives me the same error. I don't quite understand why since it's
giving u the right output. Im using the same version as you too.

If you do not mind, could you give me the .xvg file? So that I can use it as
a result. Simultaneously, I'll see what I can do to solve the problem with
your help?

Chinnu



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Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 5:47 PM, chinnu657 wrote:

md_0_1.tpr    -
production simulation .tpr file
3HTB_clean.pdb
   - .pdb
file after removing hz4 coordinates
JZ4.pdb    - jz4
coordinates
md_0_1.gro 
-production simulation .gro file
index.ndx    -
index file



The command:

echo 1 13 | g_dist -s md_0_1.tpr -f md_0_1.gro -n index.ndx

works perfectly fine for me with 4.5.5.  Try it and see what your outcome is.

-Justin

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==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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[gmx-users] Re: error with g_dist

[chinnu657]

md_0_1.tpr    -
production simulation .tpr file
3HTB_clean.pdb
   - .pdb
file after removing hz4 coordinates
JZ4.pdb    - jz4
coordinates
md_0_1.gro   
-production simulation .gro file
index.ndx    -
index file

Chinnu



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[gmx-users] Re: error with g_dist

[chinnu657]

I've copy, pasted the text after selection:

eading file md_0_1.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 33037 elements
Group 1 (Protein) has  1693 elements
Group 2 (  Protein-H) has  1301 elements
Group 3 (C-alpha) has   163 elements
Group 4 (   Backbone) has   489 elements
Group 5 (  MainChain) has   653 elements
Group 6 (   MainChain+Cb) has   805 elements
Group 7 (MainChain+H) has   815 elements
Group 8 (  SideChain) has   878 elements
Group 9 (SideChain-H) has   648 elements
Group10 (Prot-Masses) has  1693 elements
Group11 (non-Protein) has 31344 elements
Group12 (  Other) has15 elements
Group13 (JZ4) has15 elements
Group14 ( CL) has 6 elements
Group15 (  Water) has 31323 elements
Group16 (SOL) has 31323 elements
Group17 (  non-Water) has  1714 elements
Group18 (Ion) has 6 elements
Group19 (JZ4) has15 elements
Group20 ( CL) has 6 elements
Group21 ( Water_and_ions) has 31329 elements
Group22 (Protein_JZ4) has  1708 elements
Select a group: 1 13
Selected 1: 'Protein'
Select a group: Selected 13: 'JZ4'
Reading frame   0 time0.000   




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Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 5:35 PM, chinnu657 wrote:

No, I chose 1 and 13. I just tried again, but the error is still the same..



Send me your .tpr file, a coordinate file (.pdb or .gro) of the system, and your 
index file off-list and I will look into it.


-Justin

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==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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[gmx-users] Re: error with g_dist

[chinnu657]

No, I chose 1 and 13. I just tried again, but the error is still the same..

Chinnu



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Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 5:05 PM, chinnu657 wrote:

1 and 13



I don't see how this error would be possible unless you accidentally chose group 
22.  Choosing 1 and 13 should be perfectly viable.


-Justin

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==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
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jalem...@outerbanks.umaryland.edu | (410) 706-7441

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[gmx-users] Re: error with g_dist

[chinnu657]

1 and 13

Chinnu



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Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 4:58 PM, chinnu657 wrote:

Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the
protein and one being the ligand (JZ4)

screenshot.png


sorry, you may have to zoom in. I'm not sure how to snip on linux still.


Copying and pasting text works well.  I understand what the list of groups is, 
but what groups *exactly* did you choose?


-Justin

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==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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[gmx-users] Re: error with g_dist

[chinnu657]

Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the
protein and one being the ligand (JZ4)

screenshot.png
  

sorry, you may have to zoom in. I'm not sure how to snip on linux still. 
Chinnu



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Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 4:39 PM, chinnu657 wrote:

I'm basically trying to see how the distance between the ligand and protein
changes with time using their centres of mass and the only way I've come
across is by using g_dist.

I'm pasting the contents from the terminal after the doing a gmxcheck on the
md_0_1.xtc file which is my .xtc file from the production simulation.

Checking file md_0_1.xtc
Reading frame   0 time0.000
# Atoms  33037
Precision 0.001 (nm)
Last frame   1000 time 2000.000


Item#frames Timestep (ps)
Step  10012
Time  10012
Lambda   0
Coords10012
Velocities   0
Forces   0
Box   10012

can I attach the index.ndx file again? Was this what you were looking for?
index.ndx 



Better would be for you to actually tell us what groups you chose (actual screen 
output from the selection would be best), rather than leave us to scroll through 
and guess.  If md_0_1.xtc has the whole system (33037 atoms), in principle that 
error should not have occurred.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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[gmx-users] Re: error with g_dist

[chinnu657]

I'm basically trying to see how the distance between the ligand and protein
changes with time using their centres of mass and the only way I've come
across is by using g_dist.

I'm pasting the contents from the terminal after the doing a gmxcheck on the
md_0_1.xtc file which is my .xtc file from the production simulation.

Checking file md_0_1.xtc
Reading frame   0 time0.000  
# Atoms  33037
Precision 0.001 (nm)
Last frame   1000 time 2000.000  


Item#frames Timestep (ps)
Step  10012
Time  10012
Lambda   0
Coords10012
Velocities   0
Forces   0
Box   10012

can I attach the index.ndx file again? Was this what you were looking for?
index.ndx   

thank you,
chinnu



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