date:20180116




On 1/16/18 11:37 AM, Mohsen Ramezanpour wrote:

Dear Gromacs users,

In the man page of g_density for calculation of electron density, it is
mentioned that:

"The number of electrons for each atom is modified by its atomic partial
charge."

https://linux.die.net/man/1/g_density

In some publications, it seems the authors just took the atomic number as
the number of electrons for each atom name.
For instance, for POPC: they took N=7, P=15, O=8, C=6, and H=1

In some others, they did not consider the partial charge.
For instance, for POPC: they took N = 6, P = 16 and all the O atoms = 8,
C=6, and H=1

So, I was wondering which approach do you think is better?
Will the difference between these approaches matter for making conclusions?


The code accounts for the partial charges (see calc_electron_density() 
in gmx_density.cpp). You should specify the number of electrons on the 
elemental form of the atom. One cannot ascribe the entire +1 charge to N 
or -1 to P, anyway, so that's a false approach.


-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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[gmx-users] Electron density using g_density

2018-01-16 Thread Mohsen Ramezanpour

Dear Gromacs users,

In the man page of g_density for calculation of electron density, it is
mentioned that:

"The number of electrons for each atom is modified by its atomic partial
charge."

https://linux.die.net/man/1/g_density

In some publications, it seems the authors just took the atomic number as
the number of electrons for each atom name.
For instance, for POPC: they took N=7, P=15, O=8, C=6, and H=1

In some others, they did not consider the partial charge.
For instance, for POPC: they took N = 6, P = 16 and all the O atoms = 8,
C=6, and H=1

So, I was wondering which approach do you think is better?
Will the difference between these approaches matter for making conclusions?

Thanks in advance for your comments and replies
Cheers,
Mohsen

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Re: [gmx-users] difference between force constants in various force field




On 1/16/18 10:24 AM, kordza...@aut.ac.ir wrote:

Hi every one

I have a question

I want to obtain topology of carbon nano tube with x2top but I must determine 
the value of bond strength and angle constant.

I think we have a bond carbon-carbon that stretches with a constant force for 
example in amber force field this constant is 392459  kj /(mol nm^2) for 
interaction CA-CA but in gromos force field this constant is define 
differently


There is no meaningful comparison that can be made between any 
parameters in different force fields. They all use different 
parametrization conventions, and in this case you're looking at AMBER 
(all-atom) vs. GROMOS (united-atom) and therefore aspects of the atoms 
themselves will be different (e.g. heavier masses on aliphatic C in GROMOS).



I dont know what should I do

I m confused, in gromos

define gb_17   0.148.5400E+6

C,CR1,CH2

  


8.54 e 6 is force constant for stretch bond and dimention is kj/(mol nm^2), am 
I right?


No; GROMOS uses a quartic bond potential. See the manual and the 
discussion on this topic from yesterday.



then we can conclude that if I want to determine force constant , I must select 
these constant wwith respect to force field ,

I cant say these constants are same every where.rigth?

is the dimention of constant kj/(mol nm^2) every where in gromacs, such as .itp 
files of force field, itp files that we receive form ATB and so on?

any suggestion will be appreciated


If you need to develop new parameters or validate ones you have, you 
need to follow the methodology prescribed by the force field you're 
trying to use. For bonded force constants, this typically requires a QM 
vibrational frequency calculation and empirical fitting to reproduce the 
vibrational modes.


-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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[gmx-users] difference between force constants in various force field

2018-01-16 Thread kordzadeh

Hi every one

I have a question

I want to obtain topology of carbon nano tube with x2top but I must determine 
the value of bond strength and angle constant.

I think we have a bond carbon-carbon that stretches with a constant force for 
example in amber force field this constant is 392459  kj /(mol nm^2) for 
interaction CA-CA but in gromos force field this constant is define 
differently

I dont know what should I do

I m confused, in gromos

define gb_17   0.148.5400E+6

C,CR1,CH2

 

8.54 e 6 is force constant for stretch bond and dimention is kj/(mol nm^2), am 
I right?

then we can conclude that if I want to determine force constant , I must select 
these constant wwith respect to force field , 

I cant say these constants are same every where.rigth?

is the dimention of constant kj/(mol nm^2) every where in gromacs, such as .itp 
files of force field, itp files that we receive form ATB and so on?

any suggestion will be appreciated

Thank you very much

Regards

Azadeh

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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

I got it, Thank you very much for all the help!

-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 08:46 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:  Re:  Re:Can I get the fraction of solvent accessible surface 
area using "gmx sasa"?

Hi Justin,
Thank you very much!

The legend is "Total" for the command without -surface and -output. So I feel 
like if I do a division for the last columns from those two commands, I can 
just get the fraction of folded/unfolded?

e.g. 
1.467/2.767
1.824/2.757
1.901/2.736
... ...

-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 08:02 PM
To:  "gromacs.org_gmx-users";

Subject:  Re: Re:Can I get the fraction of solvent accessible surface area 
using "gmx sasa"?

Hi Justin,
Thank you very much.

So I tried:
gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns 
-surface 'group 0' -output 'group 1'

And got:
  0.000  206.8651.467
  0.100  232.4501.824
  0.200  225.9841.901

  ... ...

So my understanding is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.

But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed 
residue, so the "absolute" sasa of each residue could not reflect their buried 
extents individually.

2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns

I got:
  0.0002.767
  0.1002.757
  0.2002.736

  ... ...

Do you know what is the meaning of the second column?

Thank you!

-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 07:19 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:   Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?

Hi Alexandr,
Thank you, but it is the same with spaces between | 
:(

Cheng

-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 06:37 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:Re:  Can I get the fraction of solvent accessible surface area 
using "gmx sasa"?

Hi Justin, thank you very much.

Sorry I still do not fully understand. I have an index file, in which the group 
0 is all the residue atoms of the protein, group 1 is the first residue atoms. 
I want to calculate the sasa fraction of the residue 1. The fraction means: the 
sasa at folded state divided by the sasa when the residue is fully unfolded.

So as you said, "two selections, one for the surface, the other for what is 
output". 
) The manual says: "-surface should always consist of all non-solvent atoms in 
the system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which 
should be subsets of the calculation group", so in my case, it should be group 
1, right?

so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg 
-tu ns -surface -output

And got error message:
Error in user input:
Invalid selection '0 1 '
  Near '1'
syntax error

I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
  Near '0'
syntax error

Can you please help me? Thank you very much!
-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 04:52 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?

Thank you! So if I am using a index file, and the index 1 is the group I am 
interested, should I use the below? What is the difference between "-output" 
and "-o"?

echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns

-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users";

Subject:  Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?

Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS

Can I ask if we can use "gmx sasa" to obtain similar information? I do not like 
the "absolute" sasa, as it could not reflect the relative exposure extent of a 
residue.

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?




On 1/16/18 7:46 AM, ZHANG Cheng wrote:

Hi Justin,
Thank you very much!


The legend is "Total" for the command without -surface and -output. So I feel 
like if I do a division for the last columns from those two commands, I can just get the 
fraction of folded/unfolded?


Strictly speaking, no, because you have artificial edges of that residue 
created by ignoring the fact that there are always residues flanking it. 
And you also have no guarantee that even in an "unfolded" state that 
this residue is 100% exposed to solvent. As an approximation, sure, but 
there is some level of error that may range from negligible to 
considerable, depending entirely upon the unfolded ensemble.


-Justin



e.g.
1.467/2.767
1.824/2.757
1.901/2.736
... ...


-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 08:02 PM
To:  "gromacs.org_gmx-users";

Subject:  Re: Re:Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?



Hi Justin,
Thank you very much.


So I tried:
gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns 
-surface 'group 0' -output 'group 1'


And got:
   0.000  206.8651.467
   0.100  232.4501.824
   0.200  225.9841.901

   ... ...


So my understanding is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed residue, 
so the "absolute" sasa of each residue could not reflect their buried extents 
individually.


2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
   0.0002.767
   0.1002.757
   0.2002.736

   ... ...


Do you know what is the meaning of the second column?


Thank you!




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 07:19 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:   Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Hi Alexandr,
Thank you, but it is the same with spaces between |
:(


Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 06:37 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:Re:  Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?



Hi Justin, thank you very much.


Sorry I still do not fully understand. I have an index file, in which the group 
0 is all the residue atoms of the protein, group 1 is the first residue atoms. 
I want to calculate the sasa fraction of the residue 1. The fraction means: the 
sasa at folded state divided by the sasa when the residue is fully unfolded.


So as you said, "two selections, one for the surface, the other for what is 
output".
) The manual says: "-surface should always consist of all non-solvent atoms in the 
system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which should be 
subsets of the calculation group", so in my case, it should be group 1, right?


so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg 
-tu ns -surface -output


And got error message:
Error in user input:
Invalid selection '0 1 '
   Near '1'
 syntax error



I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
   Near '0'
 syntax error



Can you please help me? Thank you very much!
-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 04:52 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I 
use the below? What is the difference between "-output" and "-o"?


echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users";

Subject:  Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Justin,
Thank you very much!


The legend is "Total" for the command without -surface and -output. So I feel 
like if I do a division for the last columns from those two commands, I can 
just get the fraction of folded/unfolded?


e.g. 
1.467/2.767
1.824/2.757
1.901/2.736
... ...


-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 08:02 PM
To:  "gromacs.org_gmx-users";

Subject:  Re: Re:Can I get the fraction of solvent accessible surface area 
using "gmx sasa"?



Hi Justin,
Thank you very much.


So I tried:
gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns 
-surface 'group 0' -output 'group 1'


And got:
  0.000  206.8651.467
  0.100  232.4501.824
  0.200  225.9841.901

  ... ...


So my understanding is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed 
residue, so the "absolute" sasa of each residue could not reflect their buried 
extents individually.


2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
  0.0002.767
  0.1002.757
  0.2002.736

  ... ...


Do you know what is the meaning of the second column?


Thank you!




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 07:19 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:   Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?



Hi Alexandr,
Thank you, but it is the same with spaces between | 
:(


Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 06:37 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:Re:  Can I get the fraction of solvent accessible surface area 
using "gmx sasa"?



Hi Justin, thank you very much.


Sorry I still do not fully understand. I have an index file, in which the group 
0 is all the residue atoms of the protein, group 1 is the first residue atoms. 
I want to calculate the sasa fraction of the residue 1. The fraction means: the 
sasa at folded state divided by the sasa when the residue is fully unfolded.


So as you said, "two selections, one for the surface, the other for what is 
output". 
) The manual says: "-surface should always consist of all non-solvent atoms in 
the system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which 
should be subsets of the calculation group", so in my case, it should be group 
1, right?


so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg 
-tu ns -surface -output


And got error message:
Error in user input:
Invalid selection '0 1 '
  Near '1'
syntax error



I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
  Near '0'
syntax error



Can you please help me? Thank you very much!
-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 04:52 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?



Thank you! So if I am using a index file, and the index 1 is the group I am 
interested, should I use the below? What is the difference between "-output" 
and "-o"?


echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users";

Subject:  Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like 
the "absolute" sasa, as it could not reflect the relative exposure extent of a 
residue. For example, a buried big residue may have similar sasa as an exposed 
small residue.


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] six member ring won't stay flat

On 1/16/18 6:38 AM, MD wrote:

Hi Justin,

I got the itp and parameters of my side chain modified amino acid from
CHARMM-GUI and incorporated it into my protein structure, labeled with
HETATM. I made the atom types names consistent with charmm forcefield which
I used with gromacs and made sure overall the parameters look decent for
now. After some fixing the grompp would run with no warnings, and I did a
quick energy minimization, but ended up with a distorted six member ring. I
have the picture and my parameters attached. Your time is appreciated :)

https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI-rgIesxy0QdIHm7tqTug/edit?usp=sharing

You have a number of problems. If that's simply pyridoxal phosphate
linked with lysine, then you have lots of missing H atoms and the
protonation state of your phosphate group is incorrect, at least with
respect to normal physiological pH. You're getting a lot of distortion
from a lot of places, not the least of which is that you should have a
methyl group attached to the ring, not a methylene (=CH2), as that
changes the conjugation entirely.

Also, as I said before - *do not* mix CGenFF and standard CHARMM
parameters. You can't just change around atom types until grompp
warnings go away. What you're seeking to do is complicated and requires
great care, otherwise you get garbage. There's no magic push-button
here. You've got to do a thorough parametrization, including all the
things I said before. Anything short of that, in this instance, is
likely to fail. You can take initial guess charges from existing groups
in CHARMM, without even going to CGenFF, as most of those groups should
already be well described.

-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? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?




On 1/16/18 7:02 AM, ZHANG Cheng wrote:

Hi Justin,
Thank you very much.


So I tried:
gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns 
-surface 'group 0' -output 'group 1'


And got:
   0.000  206.8651.467
   0.100  232.4501.824
   0.200  225.9841.901

   ... ...


So my understanding is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed residue, 
so the "absolute" sasa of each residue could not reflect their buried extents 
individually.


gmx sasa will compute the SASA of the chosen atoms in the supplied 
configuration(s). If you want to do further manipulations, you'll have 
to script that yourself as a post-processing task.




2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
   0.0002.767
   0.1002.757
   0.2002.736

   ... ...


Do you know what is the meaning of the second column?


It should be labeled in the header of the output file, but it's the SASA 
of the chosen group of atoms, in this instance assuming that the entire 
group is solvent-exposed (because you're not computing a full surface 
here, just the SASA of the chosen atoms).


-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] rlist

2018-01-16 Thread Faezeh Pousaneh

Hi Mark,
I implement a pseudo hard sphere potential, (LJ form potential with powers
50, 49 instead of 12,6), wiht parameter sigma and epsilon parameters and
vdW cut-off=sigma.

I used Gromacs for this and is working properly for the first step. Do you
then have an idea how big should be rlist then?


Best regards


On Tue, Jan 16, 2018 at 12:51 PM, Mark Abraham 
wrote:

> Hi,
>
> That depends on what model you want to implement - rlist sets the radius
> within which particles/groups will be placed in the neighbour list. There's
> further requirements based on the other elements of the simulation with
> which it has to interact, so for user tables, the group scheme is needed,
> which means you won't have both an efficient simulation and a buffered
> list.
>
> If you're still trying to implement hard spheres with GROMACS, then as (I
> think) I've said before, you should consider alternative software (not that
> I have any insight about what might work better).
>
> Mark
>
> On Mon, Jan 15, 2018 at 11:26 AM Faezeh Pousaneh 
> wrote:
>
> > Hi,
> >
> > I have a user-potential for vdw and coulomb (PME-user). I use vdW and
> > columnb cutoffs= 0.3 and 0.5 respectively. What should be the value of
> > rlist?
> >
> > sorry, I could not find in manual.
> >
> > Best regards
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Justin,
Thank you very much.


So I tried:
gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu ns 
-surface 'group 0' -output 'group 1'


And got:
  0.000  206.8651.467
  0.100  232.4501.824
  0.200  225.9841.901

  ... ...


So my understanding is
) 1st column is the time
) 2nd column is the sasa of the whole protein
) 3rd column is the sasa of the particular group
Thank you for that.


But may I ask
1) if it is possible to calculate the fraction for a particular group in this 
way:
(sasa of the state in the xtc file)/(sasa when that group is fully unfolded)
Because a big buried residue may have similar sasa compared to a small exposed 
residue, so the "absolute" sasa of each residue could not reflect their buried 
extents individually.


2) When I do not use -surface and -output, but use echo:
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu 
ns


I got:
  0.0002.767
  0.1002.757
  0.2002.736

  ... ...


Do you know what is the meaning of the second column?


Thank you!




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 07:19 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:   Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?



Hi Alexandr,
Thank you, but it is the same with spaces between | 
:(


Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 06:37 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:Re:  Can I get the fraction of solvent accessible surface area 
using "gmx sasa"?



Hi Justin, thank you very much.


Sorry I still do not fully understand. I have an index file, in which the group 
0 is all the residue atoms of the protein, group 1 is the first residue atoms. 
I want to calculate the sasa fraction of the residue 1. The fraction means: the 
sasa at folded state divided by the sasa when the residue is fully unfolded.


So as you said, "two selections, one for the surface, the other for what is 
output". 
) The manual says: "-surface should always consist of all non-solvent atoms in 
the system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which 
should be subsets of the calculation group", so in my case, it should be group 
1, right?


so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg 
-tu ns -surface -output


And got error message:
Error in user input:
Invalid selection '0 1 '
  Near '1'
syntax error



I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
  Near '0'
syntax error



Can you please help me? Thank you very much!
-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 04:52 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?



Thank you! So if I am using a index file, and the index 1 is the group I am 
interested, should I use the below? What is the difference between "-output" 
and "-o"?


echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users";

Subject:  Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like 
the "absolute" sasa, as it could not reflect the relative exposure extent of a 
residue. For example, a buried big residue may have similar sasa as an exposed 
small residue.


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] The official release of GROMACS 2018

Hi,

Please start a new email, rather than replying to a digest and confusing
the history of the mailing list archive.

On Fri, Jan 12, 2018 at 7:05 AM Adarsh V. K. 
wrote:

> In case of Protein-ligand simulation,
>
> 1) Whether all commands used in GROMACS 5.1.4 is supported in GROMACS 2018
> also ?.
>

No, please see the release notes for the relevant intervening versions for
summary of the things changed.

> 2) Can I use a data file generated by Gromacs 5.1.4 in Gromacs 2018 to
> extend a completed protein-ligand simulation?. If yes which data file I
> should exactly copy to extend the simulation in new folder.
>

Checkpoint restarts are not supported between major version changes (we
need the ability to change the format more than users need the ability to
extend seamlessly). Otherwise, you can use gmx grompp and/or gmx
convert-tpr as normal to extend simulations. See the user guide of e.g. the
2018 documentation for some examples.

Mark

> --
> >
> > Message: 4
> > Date: Thu, 11 Jan 2018 02:30:15 +
> > From: Mark Abraham 
> > To: Discussion list for GROMACS users ,
> > " gmx-annou...@gromacs.org" 
> > Subject: [gmx-users] GROMACS 2018 official release
> > Message-ID:
> >  > gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi GROMACS users,
> >
> > The official release of GROMACS 2018 is now available.
> >
> > What new things can you expect? Please see the release notes highlights
> at
> > http://manual.gromacs.org/documentation/2018/release-notes/index.html.
> >
> > You can find the code, manual, release notes, installation instructions
> and
> > test suite at the links below.
> >
> > Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.tar.gz
> > Documentation: http://manual.gromacs.org/documentation/2018/index.html
> > (includes install guide, user guide, reference manual, and release notes)
> > Test Suite:
> http://gerrit.gromacs.org/download/regressiontests-2018.tar.gz
> >
> > Happy simulating!
> >
> > Mark Abraham
> > GROMACS development manager
> >
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Re: [gmx-users] NVML library in CUDA 9 & Gromacs 2018

Hi,

The default changed in GROMACS 2018 - even if NVML is found, we do not link
with it by default. Use cmake -DGMX_USE_NVML=on. Be advised that you may
need to take care that the nvml library found at run time is compatible
with the CUDA version used at compilation time. That can be non-trivial to
automate, so we have left that issue to users who have the desire and
ability to change the clocks (generally requires root privilege / sysadmin
approval).

Mark

On Fri, Jan 12, 2018 at 9:19 AM Jernej Zidar  wrote:

> Hi,
>
> I have an interesting problem with the  NVML library from CUDA 9 (and 9.1)
> and Gromacs 2018. Namely, the NVML is reported as detected during cmake but
> Gromacs 2018 is linked without it.
>
> This is the cmake command I would issue:
>
> m -rf * && CMAKE_PREFIX_PATH=/home/zidar/utils/fftw-3.3.6-gcc/ \
>
> cmake ../gromacs-2018-rc1 -DGMX_GPU=on -DGMX_MPI=off
> -DGMX_FFT_LIBRARY=fftw3 \
>
> -DCMAKE_INSTALL_PREFIX=/home/zidar/utils/gromacs-2018-rc1-gcc
> -DGMX_SIMD=AVX2_256
>
> make install
>
> Relevant part from cmake:
>
> -- Looking for NVIDIA GPUs present in the system
>
> -- Number of NVIDIA GPUs detected: 3
>
> -- Found CUDA: /usr/local/cuda (found suitable version "9.1", minimum
> required is "6.5")
>
> -- Found NVML: /usr/lib/x86_64-linux-gnu/libnvidia-ml.so
>
> But when I run mdrun:
>
> NOTE: GROMACS was configured without NVML support hence it can not exploit
>
>   application clocks of the detected Tesla K40c GPU to improve
> performance.
>
>   Recompile with the NVML library (compatible with the driver used) or
> set application clocks manually.
>
> CUDA is installed in /usr/local/cuda-9.1 with a symlink to /usr/local/cuda.
> The library file is physically present in /usr/lib/x86_64-linux-gnu/
>
> Gromacs 2016.4 can be compiled without issues. The NVML library is detected
> and properly linked:
>
> ldd /home/zidar/utils/gromacs-2016.4-gcc/bin/gmx
>
> linux-vdso.so.1 (0x7ffc333ad000)
>
> libgromacs.so.2 => /home/zidar/utils/gromacs-2016.4-gcc/lib/libgromacs.so.2
> (0x2ac6ada45000)
>
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x2ac6b06c2000)
>
> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x2ac6b08df000)
>
> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x2ac6b0ae3000)
>
> libnvidia-ml.so.1 => /usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1
> (0x2ac6b0ceb000)
>
> libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5
> (0x2ac6b12c5000)
>
> libfftw3f.so.3 => /home/zidar/utils/fftw-3.3.6-gcc/lib/libfftw3f.so.3
> (0x2ac6b1501000)
>
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x2ac6b1a2f000)
>
> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> (0x2ac6b1d33000)
>
> libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x2ac6b20b5000)
>
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x2ac6b22e2000)
>
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x2ac6b24f9000)
>
> /lib64/ld-linux-x86-64.so.2 (0x2ac6ad5df000)
>
> libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x2ac6b2898000)
>
> libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x2ac6b2aa3000)
>
> But not with neither Gromacs 2018 nor Gromacs 2018 rc1:
>
> ldd /home/zidar/utils/gromacs-2018-rc1-gcc/bin/gmx
>
> linux-vdso.so.1 (0x7ffd2d5fd000)
>
> libgromacs.so.3 =>
> /home/zidar/utils/gromacs-2018-rc1-gcc/lib/libgromacs.so.3
> (0x2aad09c56000)
>
> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> (0x2aad0ca83000)
>
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x2aad0ce05000)
>
> libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x2aad0d109000)
>
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x2aad0d336000)
>
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x2aad0d54d000)
>
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x2aad0d76a000)
>
> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x2aad0db09000)
>
> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x2aad0dd11000)
>
> libcufft.so.9.1 => /usr/local/cuda/lib64/libcufft.so.9.1
> (0x2aad0df15000)
>
> libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5
> (0x2aad15402000)
>
> libfftw3f.so.3 => /home/zidar/utils/fftw-3.3.6-gcc/lib/libfftw3f.so.3
> (0x2aad1563e000)
>
> /lib64/ld-linux-x86-64.so.2 (0x2aad097ed000)
>
> libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x2aad15b6c000)
>
> libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x2aad15d77000)
>
> Any idea where to start looking ?
>
> Thanks,
> Jernej
> --
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Re: [gmx-users] rlist

Hi,

That depends on what model you want to implement - rlist sets the radius
within which particles/groups will be placed in the neighbour list. There's
further requirements based on the other elements of the simulation with
which it has to interact, so for user tables, the group scheme is needed,
which means you won't have both an efficient simulation and a buffered list.

If you're still trying to implement hard spheres with GROMACS, then as (I
think) I've said before, you should consider alternative software (not that
I have any insight about what might work better).

Mark

On Mon, Jan 15, 2018 at 11:26 AM Faezeh Pousaneh 
wrote:

> Hi,
>
> I have a user-potential for vdw and coulomb (PME-user). I use vdW and
> columnb cutoffs= 0.3 and 0.5 respectively. What should be the value of
> rlist?
>
> sorry, I could not find in manual.
>
> Best regards
> --
> 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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Re: [gmx-users] six member ring won't stay flat

Hi,

You still have many sources of problems (e.g. the warnings you suppressed,
the fact that your ring's atoms interact with an environment). What happens
when you minimize a capped peptide in vacuo?

Mark

On Tue, Jan 16, 2018 at 12:39 PM MD  wrote:

> Hi Justin,
>
> I got the itp and parameters of my side chain modified amino acid from
> CHARMM-GUI and incorporated it into my protein structure, labeled with
> HETATM. I made the atom types names consistent with charmm forcefield which
> I used with gromacs and made sure overall the parameters look decent for
> now. After some fixing the grompp would run with no warnings, and I did a
> quick energy minimization, but ended up with a distorted six member ring. I
> have the picture and my parameters attached. Your time is appreciated :)
>
>
> https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI-rgIesxy0QdIHm7tqTug/edit?usp=sharing
>
> Ming
>
> On Mon, Jan 15, 2018 at 7:53 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 1/15/18 7:45 PM, MD wrote:
> >
> >> Hi Gromacs,
> >>
> >> I have a modified side chain amino acid and it has a six member ring
> >> attached to it. Regarding this ring I had dihedral angles taken care
> with
> >> some 0s and some 180s. However, after minimization my structure looks
> very
> >> strange, the ring is not flat and the dihedral angles in my settings
> >> didn't
> >> seem to apply to the minimized structure at all. Any thoughts?
> >>
> >
> > You're going to have to provide a lot more detail. You're parametrizing
> > something nonstandard, so there are plenty of places to make mistakes.
> > Without knowing your structure, the actual parameters and how derived and
> > validated them, there's nothing to do but guess.
> >
> > Keep in mind that rings are not necessarily perfectly planar, and the
> > values set for dihedral phase offsets do not strictly mean the values
> that
> > the dihedrals must adopt.
> >
> > -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!
> >
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> >
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Re: [gmx-users] six member ring won't stay flat

2018-01-16 Thread MD

Hi Justin,

I got the itp and parameters of my side chain modified amino acid from
CHARMM-GUI and incorporated it into my protein structure, labeled with
HETATM. I made the atom types names consistent with charmm forcefield which
I used with gromacs and made sure overall the parameters look decent for
now. After some fixing the grompp would run with no warnings, and I did a
quick energy minimization, but ended up with a distorted six member ring. I
have the picture and my parameters attached. Your time is appreciated :)

https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI-rgIesxy0QdIHm7tqTug/edit?usp=sharing

Ming

On Mon, Jan 15, 2018 at 7:53 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 7:45 PM, MD wrote:
>
>> Hi Gromacs,
>>
>> I have a modified side chain amino acid and it has a six member ring
>> attached to it. Regarding this ring I had dihedral angles taken care with
>> some 0s and some 180s. However, after minimization my structure looks very
>> strange, the ring is not flat and the dihedral angles in my settings
>> didn't
>> seem to apply to the minimized structure at all. Any thoughts?
>>
>
> You're going to have to provide a lot more detail. You're parametrizing
> something nonstandard, so there are plenty of places to make mistakes.
> Without knowing your structure, the actual parameters and how derived and
> validated them, there's nothing to do but guess.
>
> Keep in mind that rings are not necessarily perfectly planar, and the
> values set for dihedral phase offsets do not strictly mean the values that
> the dihedrals must adopt.
>
> -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? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?




On 1/16/18 6:19 AM, ZHANG Cheng wrote:

Hi Alexandr,
Thank you, but it is the same with spaces between |
:(


I provided the appropriate syntax before:

http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-sas

-select and -output take strings that select what you want for each. Do 
that, not echo.


-Justin



Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 06:37 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:Re:  Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?



Hi Justin, thank you very much.


Sorry I still do not fully understand. I have an index file, in which the group 
0 is all the residue atoms of the protein, group 1 is the first residue atoms. 
I want to calculate the sasa fraction of the residue 1. The fraction means: the 
sasa at folded state divided by the sasa when the residue is fully unfolded.


So as you said, "two selections, one for the surface, the other for what is 
output".
) The manual says: "-surface should always consist of all non-solvent atoms in the 
system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which should be 
subsets of the calculation group", so in my case, it should be group 1, right?


so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg 
-tu ns -surface -output


And got error message:
Error in user input:
Invalid selection '0 1 '
   Near '1'
 syntax error



I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
   Near '0'
 syntax error



Can you please help me? Thank you very much!
-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 04:52 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I 
use the below? What is the difference between "-output" and "-o"?


echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users";

Subject:  Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the 
"absolute" sasa, as it could not reflect the relative exposure extent of a residue. For 
example, a buried big residue may have similar sasa as an exposed small residue.


Thank you.


Yours sincerely
Cheng


--
==

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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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

Hi Alexandr,
Thank you, but it is the same with spaces between | 
:(


Cheng




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 06:37 PM
To:  "gromacs.org_gmx-users";

Subject:  Re:Re:  Can I get the fraction of solvent accessible surface area 
using "gmx sasa"?



Hi Justin, thank you very much.


Sorry I still do not fully understand. I have an index file, in which the group 
0 is all the residue atoms of the protein, group 1 is the first residue atoms. 
I want to calculate the sasa fraction of the residue 1. The fraction means: the 
sasa at folded state divided by the sasa when the residue is fully unfolded.


So as you said, "two selections, one for the surface, the other for what is 
output". 
) The manual says: "-surface should always consist of all non-solvent atoms in 
the system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which 
should be subsets of the calculation group", so in my case, it should be group 
1, right?


so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg 
-tu ns -surface -output


And got error message:
Error in user input:
Invalid selection '0 1 '
  Near '1'
syntax error



I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
  Near '0'
syntax error



Can you please help me? Thank you very much!
-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 04:52 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Can I get the fraction of solvent accessible surface area using 
"gmx sasa"?



Thank you! So if I am using a index file, and the index 1 is the group I am 
interested, should I use the below? What is the difference between "-output" 
and "-o"?


echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users";

Subject:  Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like 
the "absolute" sasa, as it could not reflect the relative exposure extent of a 
residue. For example, a buried big residue may have similar sasa as an exposed 
small residue.


Thank you.


Yours sincerely
Cheng
-- 
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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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

2018-01-16 Thread Alexandr Nasedkin


On 16/01/2018 11:37, ZHANG Cheng wrote:


Hi Justin, thank you very much.


Sorry I still do not fully understand. I have an index file, in which the group 
0 is all the residue atoms of the protein, group 1 is the first residue atoms. 
I want to calculate the sasa fraction of the residue 1. The fraction means: the 
sasa at folded state divided by the sasa when the residue is fully unfolded.


So as you said, "two selections, one for the surface, the other for what is 
output".
) The manual says: "-surface should always consist of all non-solvent atoms in the 
system", so in my case it should be group 0, right?
) The manual also says: "-output can specify additional selections, which should be 
subsets of the calculation group", so in my case, it should be group 1, right?


so I tried:
echo 0 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg 
-tu ns -surface -output


Try to place spaces between '|' and other arguments:
echo 0 1 | gmx sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg 
-tu ns -surface -output

and see if it works.



And got error message:
Error in user input:
Invalid selection '0 1 '
   Near '1'
 syntax error



I also tried "echo 1 0", and got the similar error:
Error in user input:
Invalid selection '1 0 '
   Near '0'
 syntax error



Can you please help me? Thank you very much!
-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 04:52 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I 
use the below? What is the difference between "-output" and "-o"?


echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users";

Subject:  Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the 
"absolute" sasa, as it could not reflect the relative exposure extent of a residue. For 
example, a buried big residue may have similar sasa as an exposed small residue.


Thank you.


Yours sincerely
Cheng

-Alexandr

--
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?