Re: [gmx-users] add atoms to gmx saxs

[Justin Lemkul]

On 2/21/18 3:33 PM, Servis, Michael wrote:

Is there a good way to add new atoms with their Cromer-Mann coefficients for 
use with gmx saxs? Thanks!


You can add entries to sfactor.dat (found in $GMXLIB).

-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

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Re: [gmx-users] Inconsistent Shifts

[Dallas Warren]

Iman,

Updating to the latest version is always a good idea.

However, the warning you have gotten doesn't actually effect any
results you obtain from running the simulation.  You simulation still
gets completed, doesn't it?  So you can actually ignore it then, and
update to the latest versions of GROMACS at a later time as
needed/able.
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 21 February 2018 at 18:56, Iman Ahmadabadi
 wrote:
> Dear Dallas,
>
> Yes, the system has periodic molecules (periodic-molecules = yes) and the
> version of gromacs is 5.1.2. So, I should use for calculating the
> properties of the system by gromacs 2016 and newer ones?
>
> Respectfully,
> Iman
>
> On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi > wrote:
>
>> Dear Gromacs users,
>>
>> In using some commands in gromacs, the sentence "There were 240
>> inconsistent shifts. Check your topology" come up on the screen and I don't
>> know what is wrong in my topology file, however it calculates correctly the
>> features of the system but I would like to know the reason of this warning.
>>
>> Respectfully,
>> Iman
>>
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[gmx-users] add atoms to gmx saxs

[Servis, Michael]

Is there a good way to add new atoms with their Cromer-Mann coefficients for 
use with gmx saxs? Thanks!


Michael

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Re: [gmx-users] Why "do_dssp" gives one more residue?

[Justin Lemkul]

On 2/21/18 1:04 PM, ZHANG Cheng wrote:

Dear Justin,
Thank you. But it does not make sense to me. Do you know if separator line is 
always all the ~ ? If the separator line is following the 214th residue, the 
215th residue should be the separator line, but why the 215th residue contains 
the secondary structure?



Maybe that's the case then. It's hard to know because the terminal 
residue in a protein is often not assigned any secondary structure. In 
older GROMACS versions, I recall the chain separator clearly showing up 
as a coil between the chains. Maybe that's not the case any more.


-Justin


You can find my files at
https://1drv.ms/f/s!AjIs-W_id1LzpOsT2Dktn9hIO7-eNA


If you use a text editor,
The 214th residue: line 248
The 215th residue: line 249


The pdb file (bfac.pdb) after the simulation is also in the link (without the 
chain ID).


The original pdb I use contains two chains. After running "gmx pdb2gmx  -f 
protein.pdb -o protein_processed.gro -water spce  -inter  -ignh -merge interactive", 
the two chains are merged to keep the inter-chain disulfide bond, and also the chain ID 
has been lost since then.


Thank you.


Yours sincerely
Cheng




-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Thu, Feb 22, 2018 01:34 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Why "do_dssp" gives one more residue?



Dear Qinghua,
Yes, exactly! But the numbering is:


1-214: first chain
215-442: second chain


However, for the secondary structure codes:


214th:
"TTSTSSSTSSSTTSTSS~SSSSSSTSSSTSTTTSTSTSTT~SS~SSSTSTTTSSTTTSSTSSTTTSSGSTTSTSSSTSSTSSTTSSTSTTSSSTSSTTTTTEEBSSEBSSTSSTSEESTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTTESET~~~SSS~SSS~~S~",


215th:
"TTST~~~TSSSTTSTSSSSSTSSSTSTTTSTSTSTT~~~TSTTT~STTTSSTSSTTTSSGSTTSTS~S~SSSTSSTSSTTTSTTSSTSTTSSSTSSTTTTTSTSSTTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTT~SSS~S",


442th:
"~~~B~~BBB~BB~BBB~B~~~B~~BT~B~B~~B",


443th: 
"~"




Do you think the 443th line is the separator? So ignore the 443th line?






-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Thu, Feb 22, 2018 01:20 AM
To:  "gromacs.org_gmx-users";"ZHANG 
Cheng"<272699...@qq.com>;

Subject:  Why "do_dssp" gives one more residue?



Dear Gromacs,
My protein only has 442 residues. After running


gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o 
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns


In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.


Can I ask why is that? Should I just ignore the 443th data?


Yours sincerely
Cheng


Here is some content copied from the ss.xpm file:


/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443   8 1",



... ...


/* y-axis:  401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 
438 439 440 441 442 443 */


--
==

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

==

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[gmx-users] installation problem

[banijamali_fs]

Hi there, 

I want to install gromacs-5.0.7 with this installation guide,

tar xfz gromacs-5.0.7.tar.gz
cd gromacs-5.0.7
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC

after running all of these commands, I type gmx to know that if this
program is correctly installed and to know
that where this program installed, but I receive this error:
gmx:error while loading shared libraries: libgromacs.so.0: cannot open
shared object file: NO such file or 
directory, I don't know what should I do? I'm totally confused, I try
many ways, but I didn't get result, please
 help me with this problem.
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Re: [gmx-users] Why "do_dssp" gives one more residue?

[ZHANG Cheng]

Dear Justin,
Thank you. But it does not make sense to me. Do you know if separator line is 
always all the ~ ? If the separator line is following the 214th residue, the 
215th residue should be the separator line, but why the 215th residue contains 
the secondary structure?


You can find my files at
https://1drv.ms/f/s!AjIs-W_id1LzpOsT2Dktn9hIO7-eNA


If you use a text editor, 
The 214th residue: line 248
The 215th residue: line 249


The pdb file (bfac.pdb) after the simulation is also in the link (without the 
chain ID). 


The original pdb I use contains two chains. After running "gmx pdb2gmx  -f 
protein.pdb -o protein_processed.gro -water spce  -inter  -ignh -merge 
interactive", the two chains are merged to keep the inter-chain disulfide bond, 
and also the chain ID has been lost since then.


Thank you.


Yours sincerely
Cheng




-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Thu, Feb 22, 2018 01:34 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Why "do_dssp" gives one more residue?



Dear Qinghua,
Yes, exactly! But the numbering is:


1-214: first chain
215-442: second chain


However, for the secondary structure codes:


214th: 
"TTSTSSSTSSSTTSTSS~SSSSSSTSSSTSTTTSTSTSTT~SS~SSSTSTTTSSTTTSSTSSTTTSSGSTTSTSSSTSSTSSTTSSTSTTSSSTSSTTTTTEEBSSEBSSTSSTSEESTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTTESET~~~SSS~SSS~~S~",


215th:
"TTST~~~TSSSTTSTSSSSSTSSSTSTTTSTSTSTT~~~TSTTT~STTTSSTSSTTTSSGSTTSTS~S~SSSTSSTSSTTTSTTSSTSTTSSSTSSTTTTTSTSSTTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTT~SSS~S",


442th:
"~~~B~~BBB~BB~BBB~B~~~B~~BT~B~B~~B",


443th: 
"~"




Do you think the 443th line is the separator? So ignore the 443th line?






-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Thu, Feb 22, 2018 01:20 AM
To:  "gromacs.org_gmx-users";"ZHANG 
Cheng"<272699...@qq.com>;

Subject:  Why "do_dssp" gives one more residue?



Dear Gromacs,
My protein only has 442 residues. After running


gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o 
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns


In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.


Can I ask why is that? Should I just ignore the 443th data?


Yours sincerely
Cheng


Here is some content copied from the ss.xpm file:


/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443   8 1",



... ...


/* y-axis:  401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 
438 439 440 441 442 443 */
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Re: [gmx-users] Why "do_dssp" gives one more residue?

[Justin Lemkul]

On 2/21/18 12:34 PM, ZHANG Cheng wrote:

Dear Qinghua,
Yes, exactly! But the numbering is:


1-214: first chain
215-442: second chain


However, for the secondary structure codes:


214th:
"TTSTSSSTSSSTTSTSS~SSSSSSTSSSTSTTTSTSTSTT~SS~SSSTSTTTSSTTTSSTSSTTTSSGSTTSTSSSTSSTSSTTSSTSTTSSSTSSTTTTTEEBSSEBSSTSSTSEESTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTTESET~~~SSS~SSS~~S~",


215th:
"TTST~~~TSSSTTSTSSSSSTSSSTSTTTSTSTSTT~~~TSTTT~STTTSSTSSTTTSSGSTTSTS~S~SSSTSSTSSTTTSTTSSTSTTSSSTSSTTTTTSTSSTTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTT~SSS~S",


442th:
"~~~B~~BBB~BB~BBB~B~~~B~~BT~B~B~~B",


443th: 
"~"




Do you think the 443th line is the separator? So ignore the 443th line?


No, the output is in the order of the coordinates: 1-214, chain 
separator, then 215-442.


-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

==

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Re: [gmx-users] Why "do_dssp" gives one more residue?

[ZHANG Cheng]

Dear Qinghua,
Yes, exactly! But the numbering is:


1-214: first chain
215-442: second chain


However, for the secondary structure codes:


214th: 
"TTSTSSSTSSSTTSTSS~SSSSSSTSSSTSTTTSTSTSTT~SS~SSSTSTTTSSTTTSSTSSTTTSSGSTTSTSSSTSSTSSTTSSTSTTSSSTSSTTTTTEEBSSEBSSTSSTSEESTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTTESET~~~SSS~SSS~~S~",


215th:
"TTST~~~TSSSTTSTSSSSSTSSSTSTTTSTSTSTT~~~TSTTT~STTTSSTSSTTTSSGSTTSTS~S~SSSTSSTSSTTTSTTSSTSTTSSSTSSTTTTTSTSSTTSTSTSTSTTTSSSTTTSTSTSSTSTTSSSTTT~SSS~S",


442th:
"~~~B~~BBB~BB~BBB~B~~~B~~BT~B~B~~B",


443th: 
"~"




Do you think the 443th line is the separator? So ignore the 443th line?






-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Thu, Feb 22, 2018 01:20 AM
To:  "gromacs.org_gmx-users";"ZHANG 
Cheng"<272699...@qq.com>;

Subject:  Why "do_dssp" gives one more residue?



Dear Gromacs,
My protein only has 442 residues. After running


gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o 
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns


In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.


Can I ask why is that? Should I just ignore the 443th data?


Yours sincerely
Cheng


Here is some content copied from the ss.xpm file:


/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443   8 1",



... ...


/* y-axis:  401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 
438 439 440 441 442 443 */
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Re: [gmx-users] Why "do_dssp" gives one more residue?

[Qinghua Liao]

Hello,

Maybe you have two chains in your system, then there should be one for 
chain separator.



Best,
Qinghua

On 02/21/2018 06:20 PM, ZHANG Cheng wrote:

Dear Gromacs,
My protein only has 442 residues. After running


gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o 
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns


In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.


Can I ask why is that? Should I just ignore the 443th data?


Yours sincerely
Cheng


Here is some content copied from the ss.xpm file:


/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443   8 1",



... ...


/* y-axis:  401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 
438 439 440 441 442 443 */



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[gmx-users] Why "do_dssp" gives one more residue?

[ZHANG Cheng]

Dear Gromacs,
My protein only has 442 residues. After running


gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o 
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns


In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 443.


Can I ask why is that? Should I just ignore the 443th data?


Yours sincerely
Cheng


Here is some content copied from the ss.xpm file:


/* x-label: "Time (ns)" */
/* y-label: "Residue" */
/* type:"Discrete" */
static char *gromacs_xpm[] = {
"317 443   8 1",



... ...


/* y-axis:  401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 
418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 
438 439 440 441 442 443 */
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Re: [gmx-users] ZNO-HSA (Human Serum albumin) Interaction

[Smith, Micholas D.]

Hard to tell from your descriptions. Things to consider:

1) Is the force-field for the ZnO particle realistic (have you validated it or 
have evidence that it is accurate)
2) If the ZnO particle has a net charge and you are running PME you are going 
to need to neutralize the system such that it accounts for both the protein and 
the ZnO nanoparticle
3) Why do you think it is wrong? What experimental evidence can you compare to 
benchmark if your results are reasonable?

We can't tell you if your results are "right or wrong," that's your 
responsibility to know this and justify it before submitting to review, but the 
questions above may help drive your thinking a bit on this.

Hope that helps. 

===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Hassan 
Aaryapour 
Sent: Wednesday, February 21, 2018 3:47 AM
To: gromacs.org_gmx-users; gmx-us...@gromacs.org
Subject: [gmx-users] ZNO-HSA (Human Serum albumin) Interaction

Dear Gromacs Users;

I am studying the toxicity effect of ZnO nanoparticle (with a partial
charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on
the Albumin structure by Gromacs. For MD simulation the nanoparticle was
placed at a distance of 1nm of protein, after running pdb2gmx, the
simulation box was solvated by TIP3P waters. The net charge of protein in
physiological condition is -14 that was neutralized by adding sodium and
chloride ions to box. Then, energy minimization, NVT and NPT were done.
>From the beginning of md simulation, the protein structure began to be
unfolded slowly before binding nanoparticle to it and after binding, the
protein structure changed dramatically. I cannot consider the charge of ZnO
as zero like silver or gold nanoparticles. So, I am confused that whether
the study method is correct or wrong for this interaction? Do the results
seem logical?

Thanks
Hassan Aryapour
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Re: [gmx-users] Calculate RDF within a certain distance from atom

[Mahsa E]

Hi,

I think the selection keywords in the manual are helpful:

http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html#selection-examples

/Mahsa


On Tue, Feb 20, 2018 at 5:53 PM, Dilip H N 
wrote:

> Hello,
> How to get RDF within a certain distance..??
>
> Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
> atoms within 0.7nm of C-alpha (Calpha-Ow).
>
> how can i get it from in-house gmx rdf command...??
>
> Any suggestions are appreciated...
>
> Thank you.
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D. Student
>
>
>
> ‌
>  Sent with Mailtrack
>  ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> medium=signature_campaign=signaturevirality>
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Re: [gmx-users] how to calculate protein-ligand interaction energy?

[Sepide Mofidifar]

 Hi Mark,
What I'm doing, is unbiased-molecular dynamics simulation. in similar to
the following reference that the interaction energy is calculated.
https://www.ncbi.nlm.nih.gov/pubmed/21545110
I think the calculation of interaction energy is favourable for these type
of studies, only I'm not sure that the summation of above options is the
right way to obtain interaction energy.

On 21 Feb 2018 14:42, "Mark Abraham"  wrote:

> Hi,
>
> You should probably follow the working a paper or tutorial that computes
> such a thing. But it probably won't give you a meaningful result, because I
> am not aware of a force field that is parameterized so that such a is
> meaningful. Computing free energy of binding would be meaningful.
>
> Mark
>
> On Wed, Feb 21, 2018 at 12:00 PM Sepide Mofidifar 
> wrote:
>
> > Dear Gromacs Users,
> > I want to calculate protein-ligand interaction energy. as far as I
> figured
> > out Its summation of these six options in gmx-energy:
> > LJ-14: Ligand-Ligand
> > Coul-14: Ligand-Ligand
> > Coul-SR: Ligand-rest
> > LJ-SR: Ligand-rest
> > Coul-LR: Ligand-rest
> > LJ-LR: Ligand-rest
> >
> > I doubt about My calculation. Therefore, it would be helpful if you
> please
> > explain in a bit more detail about calculation of interaction energy, If
> my
> > calculation method is wrong?
> >
> > Thanks
> > Sepideh Mofidifar
> > --
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> >
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> > posting!
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Re: [gmx-users] How to obtain TIP4P/? water model topology file

[Tushar Ranjan Moharana]

Hi Mark,
Thanks a lot for the suggestion. I will try it.

-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] how to calculate protein-ligand interaction energy?

[Mark Abraham]

Hi,

You should probably follow the working a paper or tutorial that computes
such a thing. But it probably won't give you a meaningful result, because I
am not aware of a force field that is parameterized so that such a is
meaningful. Computing free energy of binding would be meaningful.

Mark

On Wed, Feb 21, 2018 at 12:00 PM Sepide Mofidifar 
wrote:

> Dear Gromacs Users,
> I want to calculate protein-ligand interaction energy. as far as I figured
> out Its summation of these six options in gmx-energy:
> LJ-14: Ligand-Ligand
> Coul-14: Ligand-Ligand
> Coul-SR: Ligand-rest
> LJ-SR: Ligand-rest
> Coul-LR: Ligand-rest
> LJ-LR: Ligand-rest
>
> I doubt about My calculation. Therefore, it would be helpful if you please
> explain in a bit more detail about calculation of interaction energy, If my
> calculation method is wrong?
>
> Thanks
> Sepideh Mofidifar
> --
> 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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>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] how to calculate protein-ligand interaction energy?

[Sepide Mofidifar]

Dear Gromacs Users,
I want to calculate protein-ligand interaction energy. as far as I figured
out Its summation of these six options in gmx-energy:
LJ-14: Ligand-Ligand
Coul-14: Ligand-Ligand
Coul-SR: Ligand-rest
LJ-SR: Ligand-rest
Coul-LR: Ligand-rest
LJ-LR: Ligand-rest

I doubt about My calculation. Therefore, it would be helpful if you please
explain in a bit more detail about calculation of interaction energy, If my
calculation method is wrong?

Thanks
Sepideh Mofidifar
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Re: [gmx-users] Calculate RDF within a certain distance from atom

[João Henriques]

Justin already properly addressed the original post, so I'll just add a few
comments about the last message:

> I have the RDF between Calpha-Ow, and it is showing a slight hump/peak
around 0.47nm.

So you've managed to calculate it then as Justin suggested? FYI the RDF
minimum occurs at a larger distance for C atoms (~5 Å) than for O and N
atoms (3.3-3.5 Å), so the peak you see at 4.7 Å seems about right.

> So, i am further interested in studying how water molecules are oriented
towards it closely...what is happening around within 0.7nm distance of
Calpha w.r.t Ow...

Maybe I'm just not seeing the full picture, but how does this have anything
to do with the RDF? The RDF shows how density varies as a function of
distance from a reference particle. There certainly is some correlation
with particle orientation, but extracting this information from the RDF
profile alone seems unfeasible.

J



On Wed, Feb 21, 2018 at 5:00 AM, Dilip H N 
wrote:

> I have the RDF between Calpha-Ow, and it is showing a slight hump/peak
> around 0.47nm. So, i am further interested in studying how water molecules
> are oriented towards it closely...what is happening around within 0.7nm
> distance of Calpha w.r.t Ow...
>
> Any suggestions...??
>
> Thank you.
>
>
>
>
> ‌
>  Sent with Mailtrack
>  ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail_
> medium=signature_campaign=signaturevirality>
>
> On Tue, Feb 20, 2018 at 10:58 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 2/20/18 11:53 AM, Dilip H N wrote:
> >
> >> Hello,
> >> How to get RDF within a certain distance..??
> >>
> >> Say for eg., i have glycine amino-acid and i want the RDF of Oxygen
> water
> >> atoms within 0.7nm of C-alpha (Calpha-Ow).
> >>
> >> how can i get it from in-house gmx rdf command...??
> >>
> >
> > What do you hope to achieve from such a metric? RDF has to be normalized
> > against bulk occupancy, which will of course not be achieved at a 0.7-nm
> > distance. If you are interested in certain properties within given
> > solvation shells, distances, etc. compute the normal RDF so that it is
> > properly normalized and interpret the outcome of that calculation.
> >
> > -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
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
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[gmx-users] ZNO-HSA (Human Serum albumin) Interaction

[Hassan Aaryapour]

Dear Gromacs Users;

I am studying the toxicity effect of ZnO nanoparticle (with a partial
charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on
the Albumin structure by Gromacs. For MD simulation the nanoparticle was
placed at a distance of 1nm of protein, after running pdb2gmx, the
simulation box was solvated by TIP3P waters. The net charge of protein in
physiological condition is -14 that was neutralized by adding sodium and
chloride ions to box. Then, energy minimization, NVT and NPT were done.
>From the beginning of md simulation, the protein structure began to be
unfolded slowly before binding nanoparticle to it and after binding, the
protein structure changed dramatically. I cannot consider the charge of ZnO
as zero like silver or gold nanoparticles. So, I am confused that whether
the study method is correct or wrong for this interaction? Do the results
seem logical?

Thanks
Hassan Aryapour
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