[gmx-users] New shell water model, tabulated bonding interactions, and the documentation.

[Eric Shamay]

Over the past couple days I've attempted to implement the water model
developed by Ishiyama & Morita (J. Phys. Chem. C 2007, 111, 721-737) using a
combination of the shell polarization technique and tabulated potentials for
the bonded terms, among other things. Before elaborating below, the
documentation I found was pretty weak for the tabulated bond potentials, and
forum posts were limited in scope, so I'd like to gather some information
from those in the know such that the wiki and documentation may be updated
on this front. Furthermore, as I slowly understand and make progress, I'll
most likely post follow-ups with more questions to round out the discussion.

>From the paper above, the water model is composed of 5 sites - Oxygen (O),
Hydrogen (2x H), center of mass (G), and an auxiliary site (M) along the
bisector a distance 0.021 nm from the O. All the nonbonding terms are given,
and the intramolecular potential is as follows:

U_intra_i = Sum(n=2,6: K_n*(r1^n + r2^n)) + 1/2*K_theta*r3^2 +
K_r_theta*r3*(r1+r2) + K_r_r'*r1*r2

Where r1 and r2 are the O-H bond displacements from the equilibrium value,
and r3 is the H-H displacement. The first term is a sum with force constants
K_2, K_3,...,K_6 multiplied by the corresponding bond displacement
exponentials, and is where I planned to use a tabulated bond potential a la
the '-tableb' option for mdrun. The higher-order terms have been found
necessary for reproducing the OH vibrational red-shifting in calculated IR,
Raman, and SFG spectra. The 2nd term is the standard harmonic term but for
the H-H bond. The 3rd and 4th terms are bond-angle and bond-bond cross
terms, and are readily available in the gromacs suite already.

Turning to the tabulated potentials, this is where my questions begin. I've
calculated the 3 columns needed in a table_b0.xvg type of file: x, f(x),
f'(x) -- corresponding to the bondlength, potential, and first derivative of
the potential (a.k.a. the force), respectively. In doing so I've assumed
units of nm, kJ/mol/nm, and kJ/mol/nm^2, respectively. The function, f(x),
is as follows:

f(x) = K_2*x^2 + K_3*x^3 + K_4*x^4 + K_5*x^5 + K_6*x^6

It's rather straightforward, and gives a clean analytical solution for the
first derivative:

f'(x) = 2*K_2*x + 3*K_3*x^2 + 4*K_4*x^3 + 5*K_5*x^4 + 6*K_6*x^5

Question: Is the analytical version what I sohuld put in the 3rd column, or
should I use a finite difference method? Using the analytical version
produced a warning that my potential derivative values are an average of
164% off from the internally calculated ones - does that message mean
anything? Does it mean that I'm doing things right? Furthermore, why bother
with this 3rd column if it is something already calculated (and compared to)
by gromacs?

Using a tabspace (resolution) of 1000 datapoints per nm, I constructed a
3-column table, table_b0.xvg, and added the following to the .itp file's [
bond ] section:

[ bonds ]
; pair-potential harmonic bonds O-H terms
1 2 8 0 1.
1 3 8 0 1.

(where 1 == Oxygen; 2,3 == hydrogens)

This signifies that a lookup table will be used (with exclusions) and that
the potential will be multiplied by a force constant of 1.0 kJ/nm/mol --
effectively not changing the tabulated value.

Question: Does this all sound sane so far? Is that value of 1.0 for the
force constant actually keeping the potential term unaltered? Furthermore,
what changes if I use the function type 8(w/exclusions) vs. 9 (w/o
exclusions)?? What is being excluded if I use 8, and what does it mean if
something is excluded from bonding terms? Where are the intra-molecular
bonding exclusions defined?

Next step is to run the simulation. All is similar to previous successful
simulations in terms of my mdp input file, but I add the option of 'mdrun
-tableb table.xvg' in order to use the tabulated bond potentials for my O-H
bonds.

Question: is -tableb the only parameter needed to pass information about the
tabulated data for mdrun and simulations? Are any options necessary in the
.mdp run input file?

Once I get some confirmation about the above I'll feel confident enough to
boldly stride towards finessing the water model .itp file for sharing, and
more coherent documentation. I'm sure others have come across this issue
before, and it would be great to have some type of example fully
illustrating use of the tabulated potential data in a simulation.


~Eric
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Re: [gmx-users] New shell water model, tabulated bonding interactions, and the documentation.

[Mark Abraham]

I can help with only some of this...

- Original Message -
From: Eric Shamay 
Date: Wednesday, October 6, 2010 18:35
Subject: [gmx-users] New shell water model, tabulated bonding interactions, and 
the documentation.
To: gmx-users@gromacs.org

> Over the past couple days I've attempted to implement the water model 
> developed by Ishiyama & Morita (J. Phys. Chem. C 2007, 111, 721-737) using a 
> combination of the shell polarization technique and tabulated potentials for 
> the bonded terms, among other things. Before elaborating below, the 
> documentation I found was pretty weak for the tabulated bond potentials, and 
> forum posts were limited in scope, so I'd like to gather some information 
> from those in the know such that the wiki and documentation may be updated on 
> this front. Furthermore, as I slowly understand and make progress, I'll most 
> likely post follow-ups with more questions to round out the discussion.
 
> From the paper above, the water model is composed of 5 sites - Oxygen 
(O), Hydrogen (2x H), center of mass (G), and an auxiliary site (M) along the 
bisector a distance 0.021 nm from the O. All the nonbonding terms are given, 
and the intramolecular potential is as follows:
 > U_intra_i = Sum(n=2,6: K_n*(r1^n + r2^n)) + 1/2*K_theta*r3^2 + 
K_r_theta*r3*(r1+r2) + K_r_r'*r1*r2
> Where r1 and r2 are the O-H bond displacements from the equilibrium 
value, and r3 is the H-H displacement. The first term is a sum with force 
constants K_2, K_3,...,K_6 multiplied by the corresponding bond displacement 
exponentials, and is where I planned to use a tabulated bond potential a la the 
'-tableb' option for mdrun. The higher-order terms have been found necessary 
for reproducing the OH vibrational red-shifting in calculated IR, Raman, and 
SFG spectra. The 2nd term is the standard harmonic term but for the H-H bond. 
The 3rd and 4th terms are bond-angle and bond-bond cross terms, and are readily 
available in the gromacs suite already.
 > Turning to the tabulated potentials, this is where my questions 
begin. I've calculated the 3 columns needed in a table_b0.xvg type of file: x, 
f(x), f'(x) -- corresponding to the bondlength, potential, and first derivative 
of the potential (a.k.a. the force), respectively. In doing so I've assumed 
units of nm, kJ/mol/nm, and kJ/mol/nm^2, respectively. 



Yes, per manual 4.2.13


> The function, f(x), is as follows:
 > f(x) = K_2*x^2 + K_3*x^3 + K_4*x^4 + K_5*x^5 + K_6*x^6
> It's rather straightforward, and gives a clean analytical solution 
for the first derivative:
> f'(x) = 2*K_2*x + 3*K_3*x^2 + 4*K_4*x^3 + 5*K_5*x^4 + 6*K_6*x^5
> Question: Is the analytical version what I sohuld put in the 3rd 
column, or should I use a finite difference method? Using the analytical 
version produced a warning that my potential derivative values are an average 
of 164% off from the internally calculated ones - does that message mean 
anything? Does it mean that I'm doing things right? Furthermore, why bother 
with this 3rd column if it is something already calculated (and compared to) by 
gromacs?


I'd expect you using analytic is best, and that GROMACS is doing an internal 
finite difference calculation as a cross-check. I'm not sure why they might 
disagree...


 
> Using a tabspace (resolution) of 1000 datapoints per nm, I 
constructed a 3-column table, table_b0.xvg, and added the following to the .itp 
file's [ bond ] section:

> [ bonds ]
> ; pair-potential harmonic bonds O-H terms
> 1 2 8 0 1.
> 1 3 8 0 1.

> (where 1 == Oxygen; 2,3 == hydrogens)
> This signifies that a lookup table will be used (with exclusions) and 
that the potential will be multiplied by a force constant of 1.0 kJ/nm/mol -- 
effectively not changing the tabulated value.
 > Question: Does this all sound sane so far? 

Yes

> Is that value of 1.0 for the force constant actually keeping the potential 
> term unaltered? 
Unaltered from the table, yes.

>Furthermore, what changes if I use the function type 8(w/exclusions) vs. 9 
>(w/o exclusions)?? What is being excluded if I use 8, and what does it mean if 
>something is excluded from bonding terms? Where are the intra-molecular 
>bonding exclusions defined?
Various nonbonded terms might get excluded, but not in your case. See manual 
4.6.1 and 5.4

 > Next step is to run the simulation. All is similar to previous 
successful simulations in terms of my mdp input file, but I add the option of 
'mdrun -tableb table.xvg' in order to use the tabulated bond potentials for my 
O-H bonds. 
 > Question: is -tableb the only parameter needed to pass information 
about the tabulated data for mdrun and simulations? Are any options necessary 
in the .mdp run input file?
I would expect so. This will be straightforward to test. Run one with the old 
non-table .itp, and another with the table .itp. If you're not convinced 
something diff

[gmx-users] How can I best setup the nodes number

[#ZHAO LINA#]

Hi,

Estimate for the relative computational load of the PME mesh part: 0.33

How do I set how many nodes I should use?

#PBS -l nodes=12:ppn=4

What if the PME mesh part has different values?

is it okay? Before I did those kind of very blindly, just based on the most 
nodes I can use to hopefully run quickly.

Thanks and best regards,

lina
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Re: [gmx-users] How can I best setup the nodes number

[vinothkumar mohanakrishnan]

I think the PME mesh part is ok and it should be less than 0.5 always.

Regarding the nodes ask your administrator how many ppn one node have.
example
suppose if one node has 6 ppn then 12 nodes will have 72ppn which is
sufficient to run md.

hope the above explanation helps you.

Regards
Vinoth

On Wed, Oct 6, 2010 at 2:13 PM, #ZHAO LINA#  wrote:

>  Hi,
>
> Estimate for the relative computational load of the PME mesh part: 0.33
>
> How do I set how many nodes I should use?
>
> #PBS -l nodes=12:ppn=4
>
> What if the PME mesh part has different values?
>
> is it okay? Before I did those kind of very blindly, just based on the most
> nodes I can use to hopefully run quickly.
>
> Thanks and best regards,
>
> lina
>
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RE: [gmx-users] How can I best setup the nodes number

[#ZHAO LINA#]

I think I know how many ppn one nodes have. :-)

My question was that the number of ppn has something to do with the PME mesh 
part number or not?

Why sometimes I had a big load imbalance.

Thanks and best regards,

lina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of vinothkumar mohanakrishnan [kmvin...@gmail.com]
Sent: Wednesday, October 06, 2010 4:48 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How can I best setup the nodes number

I think the PME mesh part is ok and it should be less than 0.5 always.

Regarding the nodes ask your administrator how many ppn one node have.
example
suppose if one node has 6 ppn then 12 nodes will have 72ppn which is sufficient 
to run md.

hope the above explanation helps you.

Regards
Vinoth

On Wed, Oct 6, 2010 at 2:13 PM, #ZHAO LINA# 
mailto:zhao0...@e.ntu.edu.sg>> wrote:
Hi,

Estimate for the relative computational load of the PME mesh part: 0.33

How do I set how many nodes I should use?

#PBS -l nodes=12:ppn=4

What if the PME mesh part has different values?

is it okay? Before I did those kind of very blindly, just based on the most 
nodes I can use to hopefully run quickly.

Thanks and best regards,

lina

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Re: [gmx-users] How can I best setup the nodes number

[Mark Abraham]

- Original Message -
From: #ZHAO LINA# 
Date: Wednesday, October 6, 2010 19:44
Subject: [gmx-users] How can I best setup the nodes number
To: "gmx-users@gromacs.org" 


   P {margin-top:0;margin-bottom:0;} 
---
| 

 
 > Hi,
 > 
>  Estimate for the relative computational load of the PME mesh part: 0.33
 > 
>  How do I set how many nodes I should use?
 > 
>  #PBS -l nodes=12:ppn=4
 > 
>  What if the PME mesh part has different values?
 > 
>  is it okay? Before I did those kind of very blindly, just based on the most 
> nodes I can use to hopefully run quickly. 

There's some discussion in manual 3.17.5.

Mark
 |
---



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Re: [gmx-users] Simulations on GPU

[Szilárd Páll]

Dear Igor,

Your output look _very_ weird, it seems as if CMake internal
variable(s) were not initialized, which I have no clue how could have
happened - the build generator works just fine for me. The only thing
I can think of is that maybe your CMakeCache is corrupted.

Could you please rerun cmake in a _clean_ build directory? Also, are
you able to run cmake for CPU build (no -D options)?

--
Szilárd



On Wed, Oct 6, 2010 at 2:48 AM, Igor Leontyev  wrote:
> Szilárd wrote:
>>
>> The beta versions are all outdated, could you please use the latest
>> source distribution (4.5.1) instead (or git from the
>> release-4-5-patches branch)?
>
> The result is the same for both the distribution 4.5.1 and git from the
> release-4-5-patches. See the output bellow.
> =
>
> PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
> LD_LIBRARY_PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/lib:/home/leontyev/programs/bin/cuda/lib64:
> CPPFLAGS=-I//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/include
> -I//usr/local/opt/bin/mpi/openmpi-1.4.2/include
> LDFLAGS=-L//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/lib
> -L//usr/local/opt/bin/mpi/openmpi-1.4.2/lib
> OPENMM_ROOT_DIR=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git/openmm
>
> cmake src -DGMX_OPENMM=ON -DGMX_THREADS=OFF
> -DCMAKE_INSTALL_PREFIX=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git
> CMake Error at gmxlib/CMakeLists.txt:124 (set_target_properties):
>  set_target_properties called with incorrect number of arguments.
>
>
> CMake Error at gmxlib/CMakeLists.txt:126 (install):
>  install TARGETS given no ARCHIVE DESTINATION for static library target
>  "gmx".
>
>
> CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
>  set_target_properties called with incorrect number of arguments.
>
>
> CMake Error at mdlib/CMakeLists.txt:13 (install):
>  install TARGETS given no ARCHIVE DESTINATION for static library target
>  "md".
>
>
> CMake Error at kernel/CMakeLists.txt:43 (set_target_properties):
>  set_target_properties called with incorrect number of arguments.
>
>
> CMake Error at kernel/CMakeLists.txt:44 (set_target_properties):
>  set_target_properties called with incorrect number of arguments.
>
>
> CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18
> (CUDA_INCLUDE_DIRECTORIES):
>  Unknown CMake command "CUDA_INCLUDE_DIRECTORIES".
>
>
> CMake Warning (dev) in CMakeLists.txt:
>  No cmake_minimum_required command is present.  A line of code such as
>
>   cmake_minimum_required(VERSION 2.8)
>
>  should be added at the top of the file.  The version specified may be lower
>  if you wish to support older CMake versions for this project.  For more
>  information run "cmake --help-policy CMP".
> This warning is for project developers.  Use -Wno-dev to suppress it.
>
> -- Configuring incomplete, errors occurred!
>
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Re: [gmx-users] charmm tip5p in Gmx 4.5.2

[Szilárd Páll]

Hi,

> Does anyone have an idea about what time the Gmx 4.5.2 will be released?

Soon, if everything goes well in a matter of days.

> And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the 
> same as that in current git version?

The git branch release-4-5-patches is the branch you want to look at.
Whatever is in there will be in the release (unless it get removed :).

--
Szilárd
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RE: [gmx-users] charmm tip5p in Gmx 4.5.2

[Berk Hess]

> Date: Wed, 6 Oct 2010 11:53:56 +0200
> Subject: Re: [gmx-users] charmm tip5p in Gmx 4.5.2
> From: szilard.p...@cbr.su.se
> To: gmx-users@gromacs.org
> 
> Hi,
> 
> > Does anyone have an idea about what time the Gmx 4.5.2 will be released?
> 
> Soon, if everything goes well in a matter of days.
> 
> > And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the 
> > same as that in current git version?
> 

What is your motivation behind this question?
Do you think there is something wrong wit the current tip5p.itp?

Berk

> The git branch release-4-5-patches is the branch you want to look at.
> Whatever is in there will be in the release (unless it get removed :).
> 
> --
> Szilárd
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[gmx-users] reg. water mol. and its residence time

[babu gokul]

Dear friends 
I would like to get the water molecule residue no which is near a protein 
molecule active site and its residence time could anyone please help me in this 
regard 

Thanking you 
E R Azhagiya singam 

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Re: [gmx-users] reg. water mol. and its residence time

[Erik Marklund]

 babu gokul skrev 2010-10-06 12.27:

Dear friends
I would like to get the water molecule residue no which is near a 
protein molecule active site and its residence time could anyone 
please help me in this regard

Thanking you
E R Azhagiya singam



Try g_dist and/or g_hbond.

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] About the charge

[Anil Mhashal]

Dear friends,

please tell me, what are the possible reasons for the system total charge in
not zero and the need to neutralise it in MD simulation of the proteins.

-- 
Anil R.Mhashal
Research fellow
Physical Chemistry Division
National Chemical Laboratory
Pune
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Re: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?

[吴鹏]

Hi Mark,

Thank you for your help. Your reply gave me some hints. Firstly, I
will check again whether thread caused the problem. Then check the
requirements for code to work with threading.

The thing worries me on thread is that, Gromacs uses its own library
not the common OpenMP to manipulate thread. And there is no documents
on how to use Gromacs library. So I am a little bit worry on whether
the library is easy to use for common users. Is there any documents on
the library?
What's idea it is based on?

I will dig out what's going wrong on my code. Thank you for your help.

Best regards,

Peng
On Mon, Oct 4, 2010 at 7:55 PM, Mark Abraham  wrote:
>
>
> - Original Message -
> From: 吴鹏 
> Date: Tuesday, October 5, 2010 3:24
> Subject: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with
> multi-threading enabled?
> To: Discussion list for GROMACS users 
>
>> Dear All:
>>
>> I am trying to do trajectory analysis on-the-fly and encountered some
>> difficulty.
>>
>> What did I do:
>> I inserted a small piece of code into "md.c" to READ the
>> position of
>> atoms and do some simple analysis. In the GMX3.2, my code works fine.
>>
>> The problem:
>> In GMX4.5.1, my code works only if I set mdrun -nt to 1, i.e.
>> force GMX
>> to use one thread. Otherwise, mdrun reports segmentation fault.
>>
>> Questions:
>> 1. I speculate that the segmentation fault is caused by thread
>> conflict, i.e., I somehow break parallelization in Gromacs - is this
>> right?
>
> There are many possible causes, not least that you were using a technique
> that relied on static variables, which do not work reliably with threads.
>
>> 2. Is it possible to perform on-fly analysis or other types of
>> customization of Gromacs when multi-threading is enabled?
>
> Yes, but you have to do it right.
>
>> 3. If answer to 2 is yes, where can I find the documentations for
>> doing so, and how difficult is it to write multi-threading code using
>> Gromacs's own library?
>
> The requirements for code that works with threading are well known, and you
> should be able to Google for them. More importantly, you would have to cope
> with the problem that under domain or particle decomposition, each process
> only has a fraction of the atomic data. Unless you need the results for the
> ongoing simulation, it is far easier to write code to do your analysis
> afterwards.
>
> Mark
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] CHARMM36 Force Field

[Thomas Piggot]

Hi all,

Just to let everyone know that I have uploaded my conversion of the 
CHARMM36 force field to the GROMACS website. If you are going to use 
these files then please have a read of the forcefield.doc file for some 
more information. These lipid parameters have been checked against the 
conversion by Par Bjelkmar without any differences seen and allow the 
simulation of membrane protein systems.


If anyone has any questions (or thinks they have found any mistakes!) 
then feel free to contact me (which is probably best done through the 
mailing list).


Cheers

Tom Piggot

--
Dr Thomas Piggot
University of Southampton, UK.
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[gmx-users] do_dssp fatal error

[Paymon Pirzadeh]

Hello,
To investigate the secondary structure I issued the do_dssp command as
follows:

 do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

Then, I had read somewhere in the archive to select the alpha carbons
for accurate results, and I did, but the following error pops up:

Program do_dssp_d_mpi, VERSION 4.0.5
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
ddOD7WLo ddmJPpUs > /dev/null 2> /dev/null

The cluster technician tested the forwarded procedure (appended below),
and it seems that the backbone structure has some problems. I will be
appreciated if one tells me is it really a problem with backbone or sth
with installation of dssp. If problem is with backbone, then why pdb2gmx
did not issue any warnings?
Regards,

Paymon
--- Begin Message ---


Dear Paymon,

I have interrupted the run (it was taking too long) and I did not want to 
prevent you from work in that directory. For:
Opening library file 
/global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat

Group 0 (  System) has 293280 elements
Group 1 ( Protein) has  1002 elements
Group 2 (   Protein-H) has   485 elements
Group 3 ( C-alpha) has66 elements
Group 4 (Backbone) has   198 elements
Group 5 (   MainChain) has   265 elements
Group 6 (MainChain+Cb) has   328 elements
Group 7 ( MainChain+H) has   327 elements
Group 8 (   SideChain) has   675 elements
Group 9 ( SideChain-H) has   220 elements
Group10 ( Prot-Masses) has  1002 elements
Group11 ( Non-Protein) has 292278 elements
Group12 ( SOL) has 292278 elements
Group13 (   Other) has 292278 elements

0,1,2,5,6,7 work but
3,4,8,9,10,11,12 and 13 do not. However the output
Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na 
ddNPsTyg dda8k3CK

suggests that there is some problem with the input. So tried to run
dssp -na ddNPsTyg dda8k3CK
interactively (without do_dssp_d_mpi -f AFPIII ...) and:

dssp -na ddNPsTyg dda8k3CK
(I have used the full path i.e.:
/global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP)

the output is (I remove most of the lines as they do not seem to be 
relevant):

 !!! Backbone incomplete for residue ALA1
 residue will be ignored !!!

 !!! Backbone incomplete for residue ASN2
 residue will be ignored !!!

 !!! Backbone incomplete for residue GLN3
 residue will be ignored !!!
...
..

 !!! Backbone incomplete for residue ALA   66
 residue will be ignored !!!

 !!! HEADER-card missing !!!
 !!! COMPOUND-card missing !!!
 !!! SOURCE-card missing !!!
 !!! AUTHOR-card missing !!!
 !!! No residue with complete backbone !!!

So it once again suggests the input issue. I do not know too much about 
Gromacs and dssp setup but it clearly points to input.


All the best
Roman



On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:


Dear Roman,
do_dssp does analysis on secondary structure of proteins. It is written
on online blogs that to get the correct results, you should select alpha
carbons, option 3. However, the only problem that might be the case is
providing an index file of backbone alpha carbones which looks
irrelevant since do_dssp asks about the group interactively. I don't
know if I can try the command or not (since you mentioned it is
running), but you may try it again with group option 3.
Regards,

Paymon


On Tue, 2010-10-05 at 16:40 -0700, Roman Baranowski wrote:


Dear Paymon,

I have just log in as you, cd to:
GROMACS/proteins/AFP-III/Ih0001/81_93_204/AFPIII_Ih0001_81_93_NpT265_round1
  and issued
module load gromacs
and than:
do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

Select a group: 0
Selected 0: 'System'
There are 48779 residues in your selected group
Opening library file
/global/software/gromacs/4.0.5/intel/share/gromacs/top/ss.map
Reading frame   0 time0.000
Back Off! I just backed up ddOjBDfr to ./#ddOjBDfr.1#
Reading frame   1 time   10.000
Reading frame  50 time  500.000

and it is still running , is it possible  that there is a need for some
extra maps or databases used by dssp in the share directory.

All the best
Roman


On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:


Dear Roman,
I tried it again and the still same error:

Program do_dssp_d_mpi, VERSION 4.0.5
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
dd4qT1kw ddhRhEOb > /dev/null 2> /dev/null

The command I used was

do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

The location of 

Re: [gmx-users] do_dssp fatal error

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Hello,
To investigate the secondary structure I issued the do_dssp command as
follows:

 do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

Then, I had read somewhere in the archive to select the alpha carbons
for accurate results, and I did, but the following error pops up:



Then you read an inaccurate post.  At the very least, all MainChain atoms must 
be considered.  Think about how the DSSP algorithm works - assessment of 
hydrogen bonding patterns.  Can these patterns be determined by using only alpha 
carbons?


I know I have posted several times about how to properly use do_dssp, and it is 
also on the wiki:


http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp


Program do_dssp_d_mpi, VERSION 4.0.5
Source code file: do_dssp.c, line: 471

Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
ddOD7WLo ddmJPpUs > /dev/null 2> /dev/null

The cluster technician tested the forwarded procedure (appended below),
and it seems that the backbone structure has some problems. I will be
appreciated if one tells me is it really a problem with backbone or sth
with installation of dssp. If problem is with backbone, then why pdb2gmx
did not issue any warnings?


The results below indicate that the command works correctly for groups that 
contain all the necessary atoms.  Failures only occur when other, incorrect, 
groups are used.


-Justin


Regards,

Paymon




Subject:
RE: Sorry + Re: GROMACS utilities
From:
Roman Baranowski 
Date:
Tue, 5 Oct 2010 19:31:23 -0700 (PDT)
To:
Paymon Pirzadeh 

To:
Paymon Pirzadeh 



Dear Paymon,

I have interrupted the run (it was taking too long) and I did not want 
to prevent you from work in that directory. For:
Opening library file 
/global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat

Group 0 (  System) has 293280 elements
Group 1 ( Protein) has  1002 elements
Group 2 (   Protein-H) has   485 elements
Group 3 ( C-alpha) has66 elements
Group 4 (Backbone) has   198 elements
Group 5 (   MainChain) has   265 elements
Group 6 (MainChain+Cb) has   328 elements
Group 7 ( MainChain+H) has   327 elements
Group 8 (   SideChain) has   675 elements
Group 9 ( SideChain-H) has   220 elements
Group10 ( Prot-Masses) has  1002 elements
Group11 ( Non-Protein) has 292278 elements
Group12 ( SOL) has 292278 elements
Group13 (   Other) has 292278 elements

0,1,2,5,6,7 work but
3,4,8,9,10,11,12 and 13 do not. However the output
Fatal error:
Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na 
ddNPsTyg dda8k3CK

suggests that there is some problem with the input. So tried to run
dssp -na ddNPsTyg dda8k3CK
interactively (without do_dssp_d_mpi -f AFPIII ...) and:

dssp -na ddNPsTyg dda8k3CK
(I have used the full path i.e.:
/global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP)

the output is (I remove most of the lines as they do not seem to be 
relevant):

 !!! Backbone incomplete for residue ALA1
 residue will be ignored !!!

 !!! Backbone incomplete for residue ASN2
 residue will be ignored !!!

 !!! Backbone incomplete for residue GLN3
 residue will be ignored !!!
...
..

 !!! Backbone incomplete for residue ALA   66
 residue will be ignored !!!

 !!! HEADER-card missing !!!
 !!! COMPOUND-card missing !!!
 !!! SOURCE-card missing !!!
 !!! AUTHOR-card missing !!!
 !!! No residue with complete backbone !!!

So it once again suggests the input issue. I do not know too much about 
Gromacs and dssp setup but it clearly points to input.


All the best
Roman



On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:


Dear Roman,
do_dssp does analysis on secondary structure of proteins. It is written
on online blogs that to get the correct results, you should select alpha
carbons, option 3. However, the only problem that might be the case is
providing an index file of backbone alpha carbones which looks
irrelevant since do_dssp asks about the group interactively. I don't
know if I can try the command or not (since you mentioned it is
running), but you may try it again with group option 3.
Regards,

Paymon


On Tue, 2010-10-05 at 16:40 -0700, Roman Baranowski wrote:


 Dear Paymon,

I have just log in as you, cd to:
GROMACS/proteins/AFP-III/Ih0001/81_93_204/AFPIII_Ih0001_81_93_NpT265_round1 


  and issued
module load gromacs
and than:
do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
AFPIII_Ih0001_81_93_NpT265

Select a group: 0
Selected 0: 'System'
There are 48779 residues in your selected group
Opening library file
/global/software/gromacs/4.0.5/intel/share/gromacs/top/ss.map
Reading frame

Re: [gmx-users] do_dssp fatal error

[Paymon Pirzadeh]

Dear Justin,
Thanks a lot. Your comment was very instructive. So, I use Mainchain
(group 5) for future.

Paymon


On Wed, 2010-10-06 at 12:41 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Hello,
> > To investigate the secondary structure I issued the do_dssp command as
> > follows:
> > 
> >  do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s
> > AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump
> > AFPIII_Ih0001_81_93_NpT265
> > 
> > Then, I had read somewhere in the archive to select the alpha carbons
> > for accurate results, and I did, but the following error pops up:
> > 
> 
> Then you read an inaccurate post.  At the very least, all MainChain atoms 
> must 
> be considered.  Think about how the DSSP algorithm works - assessment of 
> hydrogen bonding patterns.  Can these patterns be determined by using only 
> alpha 
> carbons?
> 
> I know I have posted several times about how to properly use do_dssp, and it 
> is 
> also on the wiki:
> 
> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
> 
> > Program do_dssp_d_mpi, VERSION 4.0.5
> > Source code file: do_dssp.c, line: 471
> > 
> > Fatal error:
> > Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na
> > ddOD7WLo ddmJPpUs > /dev/null 2> /dev/null
> > 
> > The cluster technician tested the forwarded procedure (appended below),
> > and it seems that the backbone structure has some problems. I will be
> > appreciated if one tells me is it really a problem with backbone or sth
> > with installation of dssp. If problem is with backbone, then why pdb2gmx
> > did not issue any warnings?
> 
> The results below indicate that the command works correctly for groups that 
> contain all the necessary atoms.  Failures only occur when other, incorrect, 
> groups are used.
> 
> -Justin
> 
> > Regards,
> > 
> > Paymon
> > 
> > 
> > 
> > 
> > Subject:
> > RE: Sorry + Re: GROMACS utilities
> > From:
> > Roman Baranowski 
> > Date:
> > Tue, 5 Oct 2010 19:31:23 -0700 (PDT)
> > To:
> > Paymon Pirzadeh 
> > 
> > To:
> > Paymon Pirzadeh 
> > 
> > 
> > 
> > Dear Paymon,
> > 
> > I have interrupted the run (it was taking too long) and I did not want 
> > to prevent you from work in that directory. For:
> > Opening library file 
> > /global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat
> > Group 0 (  System) has 293280 elements
> > Group 1 ( Protein) has  1002 elements
> > Group 2 (   Protein-H) has   485 elements
> > Group 3 ( C-alpha) has66 elements
> > Group 4 (Backbone) has   198 elements
> > Group 5 (   MainChain) has   265 elements
> > Group 6 (MainChain+Cb) has   328 elements
> > Group 7 ( MainChain+H) has   327 elements
> > Group 8 (   SideChain) has   675 elements
> > Group 9 ( SideChain-H) has   220 elements
> > Group10 ( Prot-Masses) has  1002 elements
> > Group11 ( Non-Protein) has 292278 elements
> > Group12 ( SOL) has 292278 elements
> > Group13 (   Other) has 292278 elements
> > 
> > 0,1,2,5,6,7 work but
> > 3,4,8,9,10,11,12 and 13 do not. However the output
> > Fatal error:
> > Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na 
> > ddNPsTyg dda8k3CK
> > suggests that there is some problem with the input. So tried to run
> > dssp -na ddNPsTyg dda8k3CK
> > interactively (without do_dssp_d_mpi -f AFPIII ...) and:
> > 
> > dssp -na ddNPsTyg dda8k3CK
> > (I have used the full path i.e.:
> > /global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP)
> > 
> > the output is (I remove most of the lines as they do not seem to be 
> > relevant):
> >  !!! Backbone incomplete for residue ALA1
> >  residue will be ignored !!!
> > 
> >  !!! Backbone incomplete for residue ASN2
> >  residue will be ignored !!!
> > 
> >  !!! Backbone incomplete for residue GLN3
> >  residue will be ignored !!!
> > ...
> > ..
> > 
> >  !!! Backbone incomplete for residue ALA   66
> >  residue will be ignored !!!
> > 
> >  !!! HEADER-card missing !!!
> >  !!! COMPOUND-card missing !!!
> >  !!! SOURCE-card missing !!!
> >  !!! AUTHOR-card missing !!!
> >  !!! No residue with complete backbone !!!
> > 
> > So it once again suggests the input issue. I do not know too much about 
> > Gromacs and dssp setup but it clearly points to input.
> > 
> > All the best
> > Roman
> > 
> > 
> > 
> > On Tue, 5 Oct 2010, Paymon Pirzadeh wrote:
> > 
> >> Dear Roman,
> >> do_dssp does analysis on secondary structure of proteins. It is written
> >> on online blogs that to get the correct results, you should select alpha
> >> carbons, option 3. However, the only problem that might be the case is
> >> providing an index file of backbone alpha carbones which looks
> >> irrelevant since do_dssp asks about the group interactively. I don't
> >> know if I can try the comm

[gmx-users] Re: About the charge

[Vitaly Chaban]

Dear Anil:

If the charge is integer, I believe this depends only on your protein,
and you are the only one who knows the answer. If the charge is not
integer, then these are rounding errors.

-- 
Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester
Rochester, NY 14627-0216
United States of America


> Dear friends,
>
> please tell me, what are the possible reasons for the system total charge in
> not zero and the need to neutralise it in MD simulation of the proteins.
>
> --
> Anil R.Mhashal
> Research fellow
> Physical Chemistry Division
> National Chemical Laboratory
> Pune
-- 
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Re: [gmx-users] make_ndx for do_dssp

[Paymon Pirzadeh]

Hello,
I want to check the secondary structure of protein at particular residues. 
Since dssp needs all main chain atoms, does the following command at the 
make_ndx prompt makes the correct index file? 
 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 

(Main chain atom of particular residues).
regards,

Paymon

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Re: [gmx-users] make_ndx for do_dssp

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Hello, I want to check the secondary structure of protein at particular
residues. Since dssp needs all main chain atoms, does the following command
at the make_ndx prompt makes the correct index file? 


You can answer that yourself by looking at the resulting index file.


5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45



To get these groups to merge, I think you probably need to do 5 & r 1 | ...

-Justin


(Main chain atom of particular residues). regards,

Paymon



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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[gmx-users] charmm tip5p in Gmx 4.5.X

[Yao Yao]

Hi Berk,

Thanks for your reply. 

Actually I followed the fws-peptide simulation in Dr. JE Kerrigan's tutorial, 
but in charmm27 force field with tip5p water. 

Before several warnings in the simulation step, I found that even in energy 
minimization step the protein cannot be settled. I sent my mdp file to the 
forum, and got an ok from Justin. 

So I am concerned about the compatibility between tip5p and charmm force field 
in gromacs, as well as the potential improvement in the new version. 

Sincerely,

Yao

--- On Wed, 10/6/10, Berk Hess  wrote:

> From: Berk Hess 
> Subject: RE: [gmx-users] charmm tip5p in Gmx 4.5.2
> To: "Discussion list for GROMACS users" 
> Date: Wednesday, October 6, 2010, 10:02 AM
> 
> 
> 
> 
>  
> 
> 
> > Date: Wed, 6 Oct 2010 11:53:56 +0200
> > Subject: Re: [gmx-users] charmm tip5p in Gmx 4.5.2
> > From: szilard.p...@cbr.su.se
> > To: gmx-users@gromacs.org
> > 
> > Hi,
> > 
> > > Does anyone have an idea about what time the Gmx
> 4.5.2 will be released?
> > 
> > Soon, if everything goes well in a matter of days.
> > 
> > > And in 4.5.2, would the modified tip5p.itp in
> charmm27 force field be the same as that in current git
> version?
> > 
> 
> What is your motivation behind this question?
> Do you think there is something wrong wit the current
> tip5p.itp?
> 
> Berk
> 
> > The git branch release-4-5-patches is the branch you
> want to look at.
> > Whatever is in there will be in the release (unless it
> get removed :).
> > 
> > --
> > Szilárd
> > -- 
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before
> posting!
> > Please don't post (un)subscribe requests to the
> list. Use the 
> > www interface or send it to
> gmx-users-requ...@gromacs.org.
> > Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> -Inline Attachment Follows-
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Re: [gmx-users] make_ndx for do_dssp

[Paymon Pirzadeh]

Justin,
I produced the index file based on your suggestion, but when I ran the
do_dssp, a completely different result was spit out comparing to what
the whole protein analysis had given. Any ideas on why that might have
happened?

Paymon

On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Hello, I want to check the secondary structure of protein at particular
> > residues. Since dssp needs all main chain atoms, does the following command
> > at the make_ndx prompt makes the correct index file? 
> 
> You can answer that yourself by looking at the resulting index file.
> 
> > 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
> > 
> 
> To get these groups to merge, I think you probably need to do 5 & r 1 | ...
> 
> -Justin
> 
> > (Main chain atom of particular residues). regards,
> > 
> > Paymon
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 

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Re: [gmx-users] make_ndx for do_dssp

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

Justin,
I produced the index file based on your suggestion, but when I ran the
do_dssp, a completely different result was spit out comparing to what
the whole protein analysis had given. Any ideas on why that might have
happened?



That depends on what "completely different" means.  I have no idea.  If you're 
only analyzing a subset of the residues, you're going to get a discontinuous 
plot that's probably going to look a whole lot different from any analysis done 
on the whole protein.  What's more, if you're only considering small fragments 
of the protein, then omitting surrounding residues from the analysis probably 
won't permit DSSP to find hydrogen bonding partners that are necessary to 
determine the correct secondary structure.


-Justin


Paymon

On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Hello, I want to check the secondary structure of protein at particular
residues. Since dssp needs all main chain atoms, does the following command
at the make_ndx prompt makes the correct index file? 

You can answer that yourself by looking at the resulting index file.


5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45


To get these groups to merge, I think you probably need to do 5 & r 1 | ...

-Justin


(Main chain atom of particular residues). regards,

Paymon


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin







--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] charmm tip5p in Gmx 4.5.X

[Justin A. Lemkul]

Yao Yao wrote:

Hi Berk,

Thanks for your reply.

Actually I followed the fws-peptide simulation in Dr. JE Kerrigan's tutorial,
but in charmm27 force field with tip5p water.

Before several warnings in the simulation step, I found that even in energy
minimization step the protein cannot be settled. I sent my mdp file to the
forum, and got an ok from Justin.

So I am concerned about the compatibility between tip5p and charmm force
field in gromacs, as well as the potential improvement in the new version.



What improvement do you believe to exist?  The latest revision involving TIP5P 
and CHARMM (on September 10) was to remove TIP5P from the list of possible water 
models in charmm27.ff/watermodels.dat so that users wouldn't combine CHARMM + 
TIP5P.  The suggested water model for CHARMM is TIP3P.


-Justin


Sincerely,

Yao

--- On Wed, 10/6/10, Berk Hess  wrote:


From: Berk Hess  Subject: RE: [gmx-users] charmm tip5p in
Gmx 4.5.2 To: "Discussion list for GROMACS users"  
Date: Wednesday, October 6, 2010, 10:02 AM









Date: Wed, 6 Oct 2010 11:53:56 +0200 Subject: Re: [gmx-users] charmm
tip5p in Gmx 4.5.2 From: szilard.p...@cbr.su.se To: gmx-users@gromacs.org


Hi,


Does anyone have an idea about what time the Gmx

4.5.2 will be released?

Soon, if everything goes well in a matter of days.


And in 4.5.2, would the modified tip5p.itp in

charmm27 force field be the same as that in current git version? What is
your motivation behind this question? Do you think there is something wrong
wit the current tip5p.itp?

Berk


The git branch release-4-5-patches is the branch you

want to look at.

Whatever is in there will be in the release (unless it

get removed :).
-- Szilárd -- gmx-users mailing listgmx-users@gromacs.org 
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] make_ndx for do_dssp

[Paymon Pirzadeh]

I assumption was that when provide the index file, do_dssp will do the
analysis for the protein but prints out the results only for the
designated residues. All I wanted was a better resolution on the final
xpm plot to see the secondary structure of the protein at those residues
of interest. Any suggestions on how we can increase the resolution of
dssp plot and enlarging the axis of residues?
By the way, what would the option -nice do here?

Paymon 


On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote:
> 
> Paymon Pirzadeh wrote:
> > Justin,
> > I produced the index file based on your suggestion, but when I ran the
> > do_dssp, a completely different result was spit out comparing to what
> > the whole protein analysis had given. Any ideas on why that might have
> > happened?
> > 
> 
> That depends on what "completely different" means.  I have no idea.  If 
> you're 
> only analyzing a subset of the residues, you're going to get a discontinuous 
> plot that's probably going to look a whole lot different from any analysis 
> done 
> on the whole protein.  What's more, if you're only considering small 
> fragments 
> of the protein, then omitting surrounding residues from the analysis probably 
> won't permit DSSP to find hydrogen bonding partners that are necessary to 
> determine the correct secondary structure.
> 
> -Justin
> 
> > Paymon
> > 
> > On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
> >> Paymon Pirzadeh wrote:
> >>> Hello, I want to check the secondary structure of protein at particular
> >>> residues. Since dssp needs all main chain atoms, does the following 
> >>> command
> >>> at the make_ndx prompt makes the correct index file? 
> >> You can answer that yourself by looking at the resulting index file.
> >>
> >>> 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
> >>>
> >> To get these groups to merge, I think you probably need to do 5 & r 1 | ...
> >>
> >> -Justin
> >>
> >>> (Main chain atom of particular residues). regards,
> >>>
> >>> Paymon
> >>>
> >> -- 
> >> 
> >>
> >> Justin A. Lemkul
> >> Ph.D. Candidate
> >> ICTAS Doctoral Scholar
> >> MILES-IGERT Trainee
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> 
> > 
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 

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Re: [gmx-users] make_ndx for do_dssp

[Justin A. Lemkul]

Paymon Pirzadeh wrote:

I assumption was that when provide the index file, do_dssp will do the
analysis for the protein but prints out the results only for the
designated residues. All I wanted was a better resolution on the final


When prompted for only one group, that group is used for calculation and output.


xpm plot to see the secondary structure of the protein at those residues
of interest. Any suggestions on how we can increase the resolution of
dssp plot and enlarging the axis of residues?


Yes, use an .m2p file to adjust the matrix spacing.  This was discussed several 
days ago.



By the way, what would the option -nice do here?



Likely nothing.  Nice levels are irrelevant for most tasks.

-Justin

Paymon 



On Wed, 2010-10-06 at 15:29 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Justin,
I produced the index file based on your suggestion, but when I ran the
do_dssp, a completely different result was spit out comparing to what
the whole protein analysis had given. Any ideas on why that might have
happened?

That depends on what "completely different" means.  I have no idea.  If you're 
only analyzing a subset of the residues, you're going to get a discontinuous 
plot that's probably going to look a whole lot different from any analysis done 
on the whole protein.  What's more, if you're only considering small fragments 
of the protein, then omitting surrounding residues from the analysis probably 
won't permit DSSP to find hydrogen bonding partners that are necessary to 
determine the correct secondary structure.


-Justin


Paymon

On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:

Paymon Pirzadeh wrote:

Hello, I want to check the secondary structure of protein at particular
residues. Since dssp needs all main chain atoms, does the following command
at the make_ndx prompt makes the correct index file? 

You can answer that yourself by looking at the resulting index file.


5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45


To get these groups to merge, I think you probably need to do 5 & r 1 | ...

-Justin


(Main chain atom of particular residues). regards,

Paymon


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin







--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: About the charge

[Mark Abraham]

- Original Message -
From: Vitaly Chaban 
Date: Thursday, October 7, 2010 3:53
Subject: [gmx-users] Re: About the charge
To: gmx-users@gromacs.org

> Dear Anil:
> 
> If the charge is integer, I believe this depends only on your protein,
> and you are the only one who knows the answer. If the charge is not
> integer, then these are rounding errors.

... or errors from the inappropriate introduction of terminal capping groups.

Mark

> > Dear friends,
> >
> > please tell me, what are the possible reasons for the system 
> total charge in
> > not zero and the need to neutralise it in MD simulation of the 
> proteins.>
> > --
> > Anil R.Mhashal
> > Research fellow
> > Physical Chemistry Division
> > National Chemical Laboratory
> > Pune
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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